feat: replace profiles with kubernetes-style secrets

Replace the confused Profile abstraction with a dedicated Secret resource
following Kubernetes conventions. Servers now have env entries with inline
values or secretRef references. Env vars are resolved and passed to
containers at startup (fixes existing gap).

- Add Secret CRUD (model, repo, service, routes, CLI commands)
- Server env: {name, value} or {name, valueFrom: {secretRef: {name, key}}}
- Add env-resolver utility shared by instance startup and config generation
- Remove all profile-related code (models, services, routes, CLI, tests)
- Update backup/restore for secrets instead of profiles
- describe secret masks values by default, --show-values to reveal

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

docs/getting-started.md

@@ -96,10 +96,12 @@ servers:
     description: Slack MCP server
     transport: STDIO
     packageName: "@anthropic/slack-mcp"
-    envTemplate:
+    env:
       - name: SLACK_TOKEN
-        description: Slack bot token
-        isSecret: true
+        valueFrom:
+          secretRef:
+            name: slack-secrets
+            key: token
 
   - name: github
     description: GitHub MCP server

examples/ha-mcp.yaml

@@ -0,0 +1,28 @@
+servers:
+  - name: ha-mcp
+    description: "Home Assistant MCP - smart home control via MCP"
+    dockerImage: "ghcr.io/homeassistant-ai/ha-mcp:2.4"
+    transport: STREAMABLE_HTTP
+    containerPort: 3000
+    # For mcpd-managed containers:
+    command:
+      - python
+      - "-c"
+      - "from ha_mcp.server import HomeAssistantSmartMCPServer; s = HomeAssistantSmartMCPServer(); s.mcp.run(transport='sse', host='0.0.0.0', port=3000)"
+    # For connecting to an already-running instance (host.containers.internal for container-to-host):
+    externalUrl: "http://host.containers.internal:8086/mcp"
+    env:
+      - name: HOMEASSISTANT_URL
+        value: ""
+      - name: HOMEASSISTANT_TOKEN
+        valueFrom:
+          secretRef:
+            name: ha-secrets
+            key: token
+
+profiles:
+  - name: production
+    server: ha-mcp
+    envOverrides:
+      HOMEASSISTANT_URL: "https://ha.itaz.eu"
+      HOMEASSISTANT_TOKEN: "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiIyNjFlZTRhOWI2MGM0YTllOGJkNTIxN2Q3YmVmZDkzNSIsImlhdCI6MTc3MDA3NjYzOCwiZXhwIjoyMDg1NDM2NjM4fQ.17mAQxIrCBrQx3ogqAUetwEt-cngRmJiH-e7sLt-3FY"

src/cli/src/commands/apply.ts

@@ -4,6 +4,14 @@ import yaml from 'js-yaml';
 import { z } from 'zod';
 import type { ApiClient } from '../api-client.js';
 
+const ServerEnvEntrySchema = z.object({
+  name: z.string().min(1),
+  value: z.string().optional(),
+  valueFrom: z.object({
+    secretRef: z.object({ name: z.string(), key: z.string() }),
+  }).optional(),
+});
+
 const ServerSpecSchema = z.object({
   name: z.string().min(1),
   description: z.string().default(''),
@@ -11,29 +19,26 @@ const ServerSpecSchema = z.object({
   dockerImage: z.string().optional(),
   transport: z.enum(['STDIO', 'SSE', 'STREAMABLE_HTTP']).default('STDIO'),
   repositoryUrl: z.string().url().optional(),
-  envTemplate: z.array(z.object({
-    name: z.string(),
-    description: z.string().default(''),
-    isSecret: z.boolean().default(false),
-  })).default([]),
+  externalUrl: z.string().url().optional(),
+  command: z.array(z.string()).optional(),
+  containerPort: z.number().int().min(1).max(65535).optional(),
+  replicas: z.number().int().min(0).max(10).default(1),
+  env: z.array(ServerEnvEntrySchema).default([]),
 });
 
-const ProfileSpecSchema = z.object({
+const SecretSpecSchema = z.object({
   name: z.string().min(1),
-  server: z.string().min(1),
-  permissions: z.array(z.string()).default([]),
-  envOverrides: z.record(z.string()).default({}),
+  data: z.record(z.string()).default({}),
 });
 
 const ProjectSpecSchema = z.object({
   name: z.string().min(1),
   description: z.string().default(''),
-  profiles: z.array(z.string()).default([]),
 });
 
 const ApplyConfigSchema = z.object({
   servers: z.array(ServerSpecSchema).default([]),
-  profiles: z.array(ProfileSpecSchema).default([]),
+  secrets: z.array(SecretSpecSchema).default([]),
   projects: z.array(ProjectSpecSchema).default([]),
 });
 
@@ -57,7 +62,7 @@ export function createApplyCommand(deps: ApplyCommandDeps): Command {
       if (opts.dryRun) {
         log('Dry run - would apply:');
         if (config.servers.length > 0) log(`  ${config.servers.length} server(s)`);
-        if (config.profiles.length > 0) log(`  ${config.profiles.length} profile(s)`);
+        if (config.secrets.length > 0) log(`  ${config.secrets.length} secret(s)`);
         if (config.projects.length > 0) log(`  ${config.projects.length} project(s)`);
         return;
       }
@@ -80,7 +85,7 @@ function loadConfigFile(path: string): ApplyConfig {
 }
 
 async function applyConfig(client: ApiClient, config: ApplyConfig, log: (...args: unknown[]) => void): Promise<void> {
-  // Apply servers first (profiles depend on servers)
+  // Apply servers first
   for (const server of config.servers) {
     try {
       const existing = await findByName(client, 'servers', server.name);
@@ -96,34 +101,19 @@ async function applyConfig(client: ApiClient, config: ApplyConfig, log: (...args
     }
   }
 
-  // Apply profiles (need server IDs)
-  for (const profile of config.profiles) {
+  // Apply secrets
+  for (const secret of config.secrets) {
     try {
-      const server = await findByName(client, 'servers', profile.server);
-      if (!server) {
-        log(`Skipping profile '${profile.name}': server '${profile.server}' not found`);
-        continue;
-      }
-      const serverId = (server as { id: string }).id;
-
-      const existing = await findProfile(client, serverId, profile.name);
+      const existing = await findByName(client, 'secrets', secret.name);
       if (existing) {
-        await client.put(`/api/v1/profiles/${(existing as { id: string }).id}`, {
-          permissions: profile.permissions,
-          envOverrides: profile.envOverrides,
-        });
-        log(`Updated profile: ${profile.name} (server: ${profile.server})`);
+        await client.put(`/api/v1/secrets/${(existing as { id: string }).id}`, { data: secret.data });
+        log(`Updated secret: ${secret.name}`);
       } else {
-        await client.post('/api/v1/profiles', {
-          name: profile.name,
-          serverId,
-          permissions: profile.permissions,
-          envOverrides: profile.envOverrides,
-        });
-        log(`Created profile: ${profile.name} (server: ${profile.server})`);
+        await client.post('/api/v1/secrets', secret);
+        log(`Created secret: ${secret.name}`);
       }
     } catch (err) {
-      log(`Error applying profile '${profile.name}': ${err instanceof Error ? err.message : err}`);
+      log(`Error applying secret '${secret.name}': ${err instanceof Error ? err.message : err}`);
     }
   }
 
@@ -158,16 +148,5 @@ async function findByName(client: ApiClient, resource: string, name: string): Pr
   }
 }
 
-async function findProfile(client: ApiClient, serverId: string, name: string): Promise<unknown | null> {
-  try {
-    const profiles = await client.get<Array<{ name: string; serverId: string }>>(
-      `/api/v1/profiles?serverId=${serverId}`,
-    );
-    return profiles.find((p) => p.name === name) ?? null;
-  } catch {
-    return null;
-  }
-}
-
 // Export for testing
 export { loadConfigFile, applyConfig };

src/cli/src/commands/create.ts

@@ -0,0 +1,121 @@
+import { Command } from 'commander';
+import type { ApiClient } from '../api-client.js';
+export interface CreateCommandDeps {
+  client: ApiClient;
+  log: (...args: unknown[]) => void;
+}
+
+function collect(value: string, prev: string[]): string[] {
+  return [...prev, value];
+}
+
+interface ServerEnvEntry {
+  name: string;
+  value?: string;
+  valueFrom?: { secretRef: { name: string; key: string } };
+}
+
+function parseServerEnv(entries: string[]): ServerEnvEntry[] {
+  return entries.map((entry) => {
+    const eqIdx = entry.indexOf('=');
+    if (eqIdx === -1) {
+      throw new Error(`Invalid env format '${entry}'. Expected KEY=value or KEY=secretRef:SECRET:KEY`);
+    }
+    const envName = entry.slice(0, eqIdx);
+    const rhs = entry.slice(eqIdx + 1);
+
+    if (rhs.startsWith('secretRef:')) {
+      const parts = rhs.split(':');
+      if (parts.length !== 3) {
+        throw new Error(`Invalid secretRef format '${entry}'. Expected KEY=secretRef:SECRET_NAME:SECRET_KEY`);
+      }
+      return {
+        name: envName,
+        valueFrom: { secretRef: { name: parts[1]!, key: parts[2]! } },
+      };
+    }
+
+    return { name: envName, value: rhs };
+  });
+}
+
+function parseEnvEntries(entries: string[]): Record<string, string> {
+  const result: Record<string, string> = {};
+  for (const entry of entries) {
+    const eqIdx = entry.indexOf('=');
+    if (eqIdx === -1) {
+      throw new Error(`Invalid env format '${entry}'. Expected KEY=value`);
+    }
+    result[entry.slice(0, eqIdx)] = entry.slice(eqIdx + 1);
+  }
+  return result;
+}
+
+export function createCreateCommand(deps: CreateCommandDeps): Command {
+  const { client, log } = deps;
+
+  const cmd = new Command('create')
+    .description('Create a resource (server, project)');
+
+  // --- create server ---
+  cmd.command('server')
+    .description('Create an MCP server definition')
+    .argument('<name>', 'Server name (lowercase, hyphens allowed)')
+    .option('-d, --description <text>', 'Server description', '')
+    .option('--package-name <name>', 'NPM package name')
+    .option('--docker-image <image>', 'Docker image')
+    .option('--transport <type>', 'Transport type (STDIO, SSE, STREAMABLE_HTTP)', 'STDIO')
+    .option('--repository-url <url>', 'Source repository URL')
+    .option('--external-url <url>', 'External endpoint URL')
+    .option('--command <arg>', 'Command argument (repeat for multiple)', collect, [])
+    .option('--container-port <port>', 'Container port number')
+    .option('--replicas <count>', 'Number of replicas', '1')
+    .option('--env <entry>', 'Env var: KEY=value (inline) or KEY=secretRef:SECRET:KEY (secret ref, repeat for multiple)', collect, [])
+    .action(async (name: string, opts) => {
+      const body: Record<string, unknown> = {
+        name,
+        description: opts.description,
+        transport: opts.transport,
+        replicas: parseInt(opts.replicas, 10),
+      };
+      if (opts.packageName) body.packageName = opts.packageName;
+      if (opts.dockerImage) body.dockerImage = opts.dockerImage;
+      if (opts.repositoryUrl) body.repositoryUrl = opts.repositoryUrl;
+      if (opts.externalUrl) body.externalUrl = opts.externalUrl;
+      if (opts.command.length > 0) body.command = opts.command;
+      if (opts.containerPort) body.containerPort = parseInt(opts.containerPort, 10);
+      if (opts.env.length > 0) body.env = parseServerEnv(opts.env);
+
+      const server = await client.post<{ id: string; name: string }>('/api/v1/servers', body);
+      log(`server '${server.name}' created (id: ${server.id})`);
+    });
+
+  // --- create secret ---
+  cmd.command('secret')
+    .description('Create a secret')
+    .argument('<name>', 'Secret name (lowercase, hyphens allowed)')
+    .option('--data <entry>', 'Secret data KEY=value (repeat for multiple)', collect, [])
+    .action(async (name: string, opts) => {
+      const data = parseEnvEntries(opts.data);
+      const secret = await client.post<{ id: string; name: string }>('/api/v1/secrets', {
+        name,
+        data,
+      });
+      log(`secret '${secret.name}' created (id: ${secret.id})`);
+    });
+
+  // --- create project ---
+  cmd.command('project')
+    .description('Create a project')
+    .argument('<name>', 'Project name')
+    .option('-d, --description <text>', 'Project description', '')
+    .action(async (name: string, opts) => {
+      const project = await client.post<{ id: string; name: string }>('/api/v1/projects', {
+        name,
+        description: opts.description,
+      });
+      log(`project '${project.name}' created (id: ${project.id})`);
+    });
+
+  return cmd;
+}

src/cli/src/commands/delete.ts

@@ -0,0 +1,33 @@
+import { Command } from 'commander';
+import type { ApiClient } from '../api-client.js';
+import { resolveResource, resolveNameOrId } from './shared.js';
+
+export interface DeleteCommandDeps {
+  client: ApiClient;
+  log: (...args: unknown[]) => void;
+}
+
+export function createDeleteCommand(deps: DeleteCommandDeps): Command {
+  const { client, log } = deps;
+
+  return new Command('delete')
+    .description('Delete a resource (server, instance, profile, project)')
+    .argument('<resource>', 'resource type')
+    .argument('<id>', 'resource ID or name')
+    .action(async (resourceArg: string, idOrName: string) => {
+      const resource = resolveResource(resourceArg);
+
+      // Resolve name → ID for any resource type
+      let id: string;
+      try {
+        id = await resolveNameOrId(client, resource, idOrName);
+      } catch {
+        id = idOrName; // Fall through with original
+      }
+
+      await client.delete(`/api/v1/${resource}/${id}`);
+
+      const singular = resource.replace(/s$/, '');
+      log(`${singular} '${idOrName}' deleted.`);
+    });
+}

src/cli/src/commands/describe.ts

@@ -1,74 +1,227 @@
 import { Command } from 'commander';
 import { formatJson, formatYaml } from '../formatters/output.js';
+import { resolveResource, resolveNameOrId } from './shared.js';
+import type { ApiClient } from '../api-client.js';
 
 export interface DescribeCommandDeps {
+  client: ApiClient;
   fetchResource: (resource: string, id: string) => Promise<unknown>;
+  fetchInspect?: (id: string) => Promise<unknown>;
   log: (...args: string[]) => void;
 }
 
-const RESOURCE_ALIASES: Record<string, string> = {
-  server: 'servers',
-  srv: 'servers',
-  profile: 'profiles',
-  prof: 'profiles',
-  project: 'projects',
-  proj: 'projects',
-  instance: 'instances',
-  inst: 'instances',
-};
-
-function resolveResource(name: string): string {
-  const lower = name.toLowerCase();
-  return RESOURCE_ALIASES[lower] ?? lower;
+function pad(label: string, width = 18): string {
+  return label.padEnd(width);
 }
 
-function formatDetail(obj: Record<string, unknown>, indent = 0): string {
-  const pad = '  '.repeat(indent);
+function formatServerDetail(server: Record<string, unknown>): string {
   const lines: string[] = [];
+  lines.push(`=== Server: ${server.name} ===`);
+  lines.push(`${pad('Name:')}${server.name}`);
+  lines.push(`${pad('Transport:')}${server.transport ?? '-'}`);
+  lines.push(`${pad('Replicas:')}${server.replicas ?? 1}`);
+  if (server.dockerImage) lines.push(`${pad('Docker Image:')}${server.dockerImage}`);
+  if (server.packageName) lines.push(`${pad('Package:')}${server.packageName}`);
+  if (server.externalUrl) lines.push(`${pad('External URL:')}${server.externalUrl}`);
+  if (server.repositoryUrl) lines.push(`${pad('Repository:')}${server.repositoryUrl}`);
+  if (server.containerPort) lines.push(`${pad('Container Port:')}${server.containerPort}`);
+  if (server.description) lines.push(`${pad('Description:')}${server.description}`);
 
-  for (const [key, value] of Object.entries(obj)) {
-    if (value === null || value === undefined) {
-      lines.push(`${pad}${key}: -`);
-    } else if (Array.isArray(value)) {
-      if (value.length === 0) {
-        lines.push(`${pad}${key}: []`);
-      } else if (typeof value[0] === 'object') {
-        lines.push(`${pad}${key}:`);
-        for (const item of value) {
-          lines.push(`${pad}  - ${JSON.stringify(item)}`);
-        }
-      } else {
-        lines.push(`${pad}${key}: ${value.join(', ')}`);
+  const command = server.command as string[] | null;
+  if (command && command.length > 0) {
+    lines.push('');
+    lines.push('Command:');
+    lines.push(`  ${command.join(' ')}`);
+  }
+
+  const env = server.env as Array<{ name: string; value?: string; valueFrom?: { secretRef: { name: string; key: string } } }> | undefined;
+  if (env && env.length > 0) {
+    lines.push('');
+    lines.push('Environment:');
+    const nameW = Math.max(6, ...env.map((e) => e.name.length)) + 2;
+    lines.push(`  ${'NAME'.padEnd(nameW)}SOURCE`);
+    for (const e of env) {
+      if (e.value !== undefined) {
+        lines.push(`  ${e.name.padEnd(nameW)}${e.value}`);
+      } else if (e.valueFrom?.secretRef) {
+        const ref = e.valueFrom.secretRef;
+        lines.push(`  ${e.name.padEnd(nameW)}secret:${ref.name}/${ref.key}`);
       }
-    } else if (typeof value === 'object') {
-      lines.push(`${pad}${key}:`);
-      lines.push(formatDetail(value as Record<string, unknown>, indent + 1));
-    } else {
-      lines.push(`${pad}${key}: ${String(value)}`);
     }
   }
 
+  lines.push('');
+  lines.push('Metadata:');
+  lines.push(`  ${pad('ID:', 12)}${server.id}`);
+  if (server.createdAt) lines.push(`  ${pad('Created:', 12)}${server.createdAt}`);
+  if (server.updatedAt) lines.push(`  ${pad('Updated:', 12)}${server.updatedAt}`);
+
+  return lines.join('\n');
+}
+
+function formatInstanceDetail(instance: Record<string, unknown>, inspect?: Record<string, unknown>): string {
+  const lines: string[] = [];
+  lines.push(`=== Instance: ${instance.id} ===`);
+  lines.push(`${pad('Status:')}${instance.status}`);
+  lines.push(`${pad('Server ID:')}${instance.serverId}`);
+  lines.push(`${pad('Container ID:')}${instance.containerId ?? '-'}`);
+  lines.push(`${pad('Port:')}${instance.port ?? '-'}`);
+
+  const metadata = instance.metadata as Record<string, unknown> | undefined;
+  if (metadata && Object.keys(metadata).length > 0) {
+    lines.push('');
+    lines.push('Metadata:');
+    for (const [key, value] of Object.entries(metadata)) {
+      lines.push(`  ${pad(key + ':', 16)}${String(value)}`);
+    }
+  }
+
+  if (inspect) {
+    lines.push('');
+    lines.push('Container:');
+    for (const [key, value] of Object.entries(inspect)) {
+      if (typeof value === 'object' && value !== null) {
+        lines.push(`  ${key}: ${JSON.stringify(value)}`);
+      } else {
+        lines.push(`  ${pad(key + ':', 16)}${String(value)}`);
+      }
+    }
+  }
+
+  lines.push('');
+  lines.push(`  ${pad('ID:', 12)}${instance.id}`);
+  if (instance.createdAt) lines.push(`  ${pad('Created:', 12)}${instance.createdAt}`);
+  if (instance.updatedAt) lines.push(`  ${pad('Updated:', 12)}${instance.updatedAt}`);
+
+  return lines.join('\n');
+}
+
+function formatProjectDetail(project: Record<string, unknown>): string {
+  const lines: string[] = [];
+  lines.push(`=== Project: ${project.name} ===`);
+  lines.push(`${pad('Name:')}${project.name}`);
+  if (project.description) lines.push(`${pad('Description:')}${project.description}`);
+  if (project.ownerId) lines.push(`${pad('Owner:')}${project.ownerId}`);
+
+  lines.push('');
+  lines.push('Metadata:');
+  lines.push(`  ${pad('ID:', 12)}${project.id}`);
+  if (project.createdAt) lines.push(`  ${pad('Created:', 12)}${project.createdAt}`);
+  if (project.updatedAt) lines.push(`  ${pad('Updated:', 12)}${project.updatedAt}`);
+
+  return lines.join('\n');
+}
+
+function formatSecretDetail(secret: Record<string, unknown>, showValues: boolean): string {
+  const lines: string[] = [];
+  lines.push(`=== Secret: ${secret.name} ===`);
+  lines.push(`${pad('Name:')}${secret.name}`);
+
+  const data = secret.data as Record<string, string> | undefined;
+  if (data && Object.keys(data).length > 0) {
+    lines.push('');
+    lines.push('Data:');
+    const keyW = Math.max(4, ...Object.keys(data).map((k) => k.length)) + 2;
+    for (const [key, value] of Object.entries(data)) {
+      const display = showValues ? value : '***';
+      lines.push(`  ${key.padEnd(keyW)}${display}`);
+    }
+    if (!showValues) {
+      lines.push('');
+      lines.push('  (use --show-values to reveal)');
+    }
+  } else {
+    lines.push(`${pad('Data:')}(empty)`);
+  }
+
+  lines.push('');
+  lines.push('Metadata:');
+  lines.push(`  ${pad('ID:', 12)}${secret.id}`);
+  if (secret.createdAt) lines.push(`  ${pad('Created:', 12)}${secret.createdAt}`);
+  if (secret.updatedAt) lines.push(`  ${pad('Updated:', 12)}${secret.updatedAt}`);
+
+  return lines.join('\n');
+}
+
+function formatGenericDetail(obj: Record<string, unknown>): string {
+  const lines: string[] = [];
+  for (const [key, value] of Object.entries(obj)) {
+    if (value === null || value === undefined) {
+      lines.push(`${pad(key + ':')}  -`);
+    } else if (Array.isArray(value)) {
+      if (value.length === 0) {
+        lines.push(`${pad(key + ':')}  []`);
+      } else {
+        lines.push(`${key}:`);
+        for (const item of value) {
+          lines.push(`  - ${typeof item === 'object' ? JSON.stringify(item) : String(item)}`);
+        }
+      }
+    } else if (typeof value === 'object') {
+      lines.push(`${key}:`);
+      for (const [k, v] of Object.entries(value as Record<string, unknown>)) {
+        lines.push(`  ${pad(k + ':')}${String(v)}`);
+      }
+    } else {
+      lines.push(`${pad(key + ':')}${String(value)}`);
+    }
+  }
   return lines.join('\n');
 }
 
 export function createDescribeCommand(deps: DescribeCommandDeps): Command {
   return new Command('describe')
     .description('Show detailed information about a resource')
-    .argument('<resource>', 'resource type (server, profile, project, instance)')
-    .argument('<id>', 'resource ID')
+    .argument('<resource>', 'resource type (server, project, instance)')
+    .argument('<id>', 'resource ID or name')
     .option('-o, --output <format>', 'output format (detail, json, yaml)', 'detail')
-    .action(async (resourceArg: string, id: string, opts: { output: string }) => {
+    .option('--show-values', 'Show secret values (default: masked)')
+    .action(async (resourceArg: string, idOrName: string, opts: { output: string; showValues?: boolean }) => {
       const resource = resolveResource(resourceArg);
-      const item = await deps.fetchResource(resource, id);
+
+      // Resolve name → ID
+      let id: string;
+      try {
+        id = await resolveNameOrId(deps.client, resource, idOrName);
+      } catch {
+        id = idOrName;
+      }
+
+      const item = await deps.fetchResource(resource, id) as Record<string, unknown>;
+
+      // Enrich instances with container inspect data
+      let inspect: Record<string, unknown> | undefined;
+      if (resource === 'instances' && deps.fetchInspect && item.containerId) {
+        try {
+          inspect = await deps.fetchInspect(id) as Record<string, unknown>;
+          item.containerInspect = inspect;
+        } catch {
+          // Container may not be available
+        }
+      }
 
       if (opts.output === 'json') {
         deps.log(formatJson(item));
       } else if (opts.output === 'yaml') {
         deps.log(formatYaml(item));
       } else {
-        const typeName = resource.replace(/s$/, '').charAt(0).toUpperCase() + resource.replace(/s$/, '').slice(1);
-        deps.log(`--- ${typeName} ---`);
-        deps.log(formatDetail(item as Record<string, unknown>));
+        // Visually clean sectioned output
+        switch (resource) {
+          case 'servers':
+            deps.log(formatServerDetail(item));
+            break;
+          case 'instances':
+            deps.log(formatInstanceDetail(item, inspect));
+            break;
+          case 'secrets':
+            deps.log(formatSecretDetail(item, opts.showValues === true));
+            break;
+          case 'projects':
+            deps.log(formatProjectDetail(item));
+            break;
+          default:
+            deps.log(formatGenericDetail(item));
+        }
       }
     });
 }

src/cli/src/commands/edit.ts

@@ -0,0 +1,114 @@
+import { Command } from 'commander';
+import { writeFileSync, readFileSync, unlinkSync, mkdtempSync } from 'node:fs';
+import { join } from 'node:path';
+import { tmpdir } from 'node:os';
+import { execSync } from 'node:child_process';
+import yaml from 'js-yaml';
+import type { ApiClient } from '../api-client.js';
+import { resolveResource, resolveNameOrId, stripInternalFields } from './shared.js';
+
+export interface EditCommandDeps {
+  client: ApiClient;
+  log: (...args: unknown[]) => void;
+  /** Override for testing — return editor binary name. */
+  getEditor?: () => string;
+  /** Override for testing — simulate opening the editor. */
+  openEditor?: (filePath: string, editor: string) => void;
+}
+
+function getEditor(deps: EditCommandDeps): string {
+  if (deps.getEditor) return deps.getEditor();
+  return process.env.VISUAL ?? process.env.EDITOR ?? 'vi';
+}
+
+function openEditor(filePath: string, editor: string, deps: EditCommandDeps): void {
+  if (deps.openEditor) {
+    deps.openEditor(filePath, editor);
+    return;
+  }
+  execSync(`${editor} "${filePath}"`, { stdio: 'inherit' });
+}
+
+export function createEditCommand(deps: EditCommandDeps): Command {
+  const { client, log } = deps;
+
+  return new Command('edit')
+    .description('Edit a resource in your default editor (server, project)')
+    .argument('<resource>', 'Resource type (server, project)')
+    .argument('<name-or-id>', 'Resource name or ID')
+    .action(async (resourceArg: string, nameOrId: string) => {
+      const resource = resolveResource(resourceArg);
+
+      // Instances are immutable
+      if (resource === 'instances') {
+        log('Error: instances are immutable and cannot be edited.');
+        log('To change an instance, update the server definition and let reconciliation handle it.');
+        process.exitCode = 1;
+        return;
+      }
+
+      const validResources = ['servers', 'secrets', 'projects'];
+      if (!validResources.includes(resource)) {
+        log(`Error: unknown resource type '${resourceArg}'`);
+        process.exitCode = 1;
+        return;
+      }
+
+      // Resolve name → ID
+      const id = await resolveNameOrId(client, resource, nameOrId);
+
+      // Fetch current state
+      const current = await client.get<Record<string, unknown>>(`/api/v1/${resource}/${id}`);
+
+      // Strip read-only fields for editor
+      const editable = stripInternalFields(current);
+
+      // Serialize to YAML
+      const singular = resource.replace(/s$/, '');
+      const header = `# Editing ${singular}: ${nameOrId}\n# Save and close to apply changes. Clear the file to cancel.\n`;
+      const originalYaml = yaml.dump(editable, { lineWidth: 120, noRefs: true });
+      const content = header + originalYaml;
+
+      // Write to temp file
+      const tmpDir = mkdtempSync(join(tmpdir(), 'mcpctl-edit-'));
+      const tmpFile = join(tmpDir, `${singular}-${nameOrId}.yaml`);
+      writeFileSync(tmpFile, content, 'utf-8');
+
+      try {
+        // Open editor
+        const editor = getEditor(deps);
+        openEditor(tmpFile, editor, deps);
+
+        // Read back
+        const modified = readFileSync(tmpFile, 'utf-8');
+
+        // Strip comments for comparison
+        const modifiedClean = modified
+          .split('\n')
+          .filter((line) => !line.startsWith('#'))
+          .join('\n')
+          .trim();
+
+        if (!modifiedClean) {
+          log('Edit cancelled (empty file).');
+          return;
+        }
+
+        if (modifiedClean === originalYaml.trim()) {
+          log(`${singular} '${nameOrId}' unchanged.`);
+          return;
+        }
+
+        // Parse and apply
+        const updates = yaml.load(modifiedClean) as Record<string, unknown>;
+        await client.put(`/api/v1/${resource}/${id}`, updates);
+        log(`${singular} '${nameOrId}' updated.`);
+      } finally {
+        try {
+          unlinkSync(tmpFile);
+        } catch {
+          // Ignore cleanup errors
+        }
+      }
+    });
+}

src/cli/src/commands/get.ts

@@ -2,6 +2,7 @@ import { Command } from 'commander';
 import { formatTable } from '../formatters/table.js';
 import { formatJson, formatYaml } from '../formatters/output.js';
 import type { Column } from '../formatters/table.js';
+import { resolveResource, stripInternalFields } from './shared.js';
 
 export interface GetCommandDeps {
   fetchResource: (resource: string, id?: string) => Promise<unknown[]>;
@@ -16,12 +17,6 @@ interface ServerRow {
   dockerImage: string | null;
 }
 
-interface ProfileRow {
-  id: string;
-  name: string;
-  serverId: string;
-}
-
 interface ProjectRow {
   id: string;
   name: string;
@@ -29,6 +24,12 @@ interface ProjectRow {
   ownerId: string;
 }
 
+interface SecretRow {
+  id: string;
+  name: string;
+  data: Record<string, string>;
+}
+
 interface InstanceRow {
   id: string;
   serverId: string;
@@ -37,22 +38,6 @@ interface InstanceRow {
   port: number | null;
 }
 
-const RESOURCE_ALIASES: Record<string, string> = {
-  server: 'servers',
-  srv: 'servers',
-  profile: 'profiles',
-  prof: 'profiles',
-  project: 'projects',
-  proj: 'projects',
-  instance: 'instances',
-  inst: 'instances',
-};
-
-function resolveResource(name: string): string {
-  const lower = name.toLowerCase();
-  return RESOURCE_ALIASES[lower] ?? lower;
-}
-
 const serverColumns: Column<ServerRow>[] = [
   { header: 'NAME', key: 'name' },
   { header: 'TRANSPORT', key: 'transport', width: 16 },
@@ -61,12 +46,6 @@ const serverColumns: Column<ServerRow>[] = [
   { header: 'ID', key: 'id' },
 ];
 
-const profileColumns: Column<ProfileRow>[] = [
-  { header: 'NAME', key: 'name' },
-  { header: 'SERVER ID', key: 'serverId' },
-  { header: 'ID', key: 'id' },
-];
-
 const projectColumns: Column<ProjectRow>[] = [
   { header: 'NAME', key: 'name' },
   { header: 'DESCRIPTION', key: 'description', width: 40 },
@@ -74,6 +53,12 @@ const projectColumns: Column<ProjectRow>[] = [
   { header: 'ID', key: 'id' },
 ];
 
+const secretColumns: Column<SecretRow>[] = [
+  { header: 'NAME', key: 'name' },
+  { header: 'KEYS', key: (r) => Object.keys(r.data).join(', ') || '-', width: 40 },
+  { header: 'ID', key: 'id' },
+];
+
 const instanceColumns: Column<InstanceRow>[] = [
   { header: 'STATUS', key: 'status', width: 10 },
   { header: 'SERVER ID', key: 'serverId' },
@@ -86,10 +71,10 @@ function getColumnsForResource(resource: string): Column<Record<string, unknown>
   switch (resource) {
     case 'servers':
       return serverColumns as unknown as Column<Record<string, unknown>>[];
-    case 'profiles':
-      return profileColumns as unknown as Column<Record<string, unknown>>[];
     case 'projects':
       return projectColumns as unknown as Column<Record<string, unknown>>[];
+    case 'secrets':
+      return secretColumns as unknown as Column<Record<string, unknown>>[];
     case 'instances':
       return instanceColumns as unknown as Column<Record<string, unknown>>[];
     default:
@@ -100,21 +85,38 @@ function getColumnsForResource(resource: string): Column<Record<string, unknown>
   }
 }
 
+/**
+ * Transform API response items into apply-compatible format.
+ * Strips internal fields and wraps in the resource key.
+ */
+function toApplyFormat(resource: string, items: unknown[]): Record<string, unknown[]> {
+  const cleaned = items.map((item) => {
+    return stripInternalFields(item as Record<string, unknown>);
+  });
+  return { [resource]: cleaned };
+}
+
 export function createGetCommand(deps: GetCommandDeps): Command {
   return new Command('get')
-    .description('List resources (servers, profiles, projects, instances)')
-    .argument('<resource>', 'resource type (servers, profiles, projects, instances)')
-    .argument('[id]', 'specific resource ID')
+    .description('List resources (servers, projects, instances)')
+    .argument('<resource>', 'resource type (servers, projects, instances)')
+    .argument('[id]', 'specific resource ID or name')
     .option('-o, --output <format>', 'output format (table, json, yaml)', 'table')
     .action(async (resourceArg: string, id: string | undefined, opts: { output: string }) => {
       const resource = resolveResource(resourceArg);
       const items = await deps.fetchResource(resource, id);
 
       if (opts.output === 'json') {
-        deps.log(formatJson(items.length === 1 ? items[0] : items));
+        // Apply-compatible JSON wrapped in resource key
+        deps.log(formatJson(toApplyFormat(resource, items)));
       } else if (opts.output === 'yaml') {
-        deps.log(formatYaml(items.length === 1 ? items[0] : items));
+        // Apply-compatible YAML wrapped in resource key
+        deps.log(formatYaml(toApplyFormat(resource, items)));
       } else {
+        if (items.length === 0) {
+          deps.log(`No ${resource} found.`);
+          return;
+        }
         const columns = getColumnsForResource(resource);
         deps.log(formatTable(items as Record<string, unknown>[], columns));
       }

src/cli/src/commands/instances.ts

@@ -1,123 +0,0 @@
-import { Command } from 'commander';
-import type { ApiClient } from '../api-client.js';
-
-interface Instance {
-  id: string;
-  serverId: string;
-  status: string;
-  containerId: string | null;
-  port: number | null;
-  createdAt: string;
-}
-
-export interface InstanceCommandDeps {
-  client: ApiClient;
-  log: (...args: unknown[]) => void;
-}
-
-export function createInstanceCommands(deps: InstanceCommandDeps): Command {
-  const { client, log } = deps;
-  const cmd = new Command('instance')
-    .alias('instances')
-    .alias('inst')
-    .description('Manage MCP server instances');
-
-  cmd
-    .command('list')
-    .alias('ls')
-    .description('List running instances')
-    .option('-s, --server <id>', 'Filter by server ID')
-    .option('-o, --output <format>', 'Output format (table, json)', 'table')
-    .action(async (opts: { server?: string; output: string }) => {
-      let url = '/api/v1/instances';
-      if (opts.server) {
-        url += `?serverId=${encodeURIComponent(opts.server)}`;
-      }
-      const instances = await client.get<Instance[]>(url);
-      if (opts.output === 'json') {
-        log(JSON.stringify(instances, null, 2));
-        return;
-      }
-      if (instances.length === 0) {
-        log('No instances found.');
-        return;
-      }
-      log('ID\tSERVER\tSTATUS\tPORT\tCONTAINER');
-      for (const inst of instances) {
-        const cid = inst.containerId ? inst.containerId.slice(0, 12) : '-';
-        const port = inst.port ?? '-';
-        log(`${inst.id}\t${inst.serverId}\t${inst.status}\t${port}\t${cid}`);
-      }
-    });
-
-  cmd
-    .command('start <serverId>')
-    .description('Start a new MCP server instance')
-    .option('-p, --port <port>', 'Host port to bind')
-    .option('-o, --output <format>', 'Output format (table, json)', 'table')
-    .action(async (serverId: string, opts: { port?: string; output: string }) => {
-      const body: Record<string, unknown> = { serverId };
-      if (opts.port !== undefined) {
-        body.hostPort = parseInt(opts.port, 10);
-      }
-      const instance = await client.post<Instance>('/api/v1/instances', body);
-      if (opts.output === 'json') {
-        log(JSON.stringify(instance, null, 2));
-        return;
-      }
-      log(`Instance ${instance.id} started (status: ${instance.status})`);
-    });
-
-  cmd
-    .command('stop <id>')
-    .description('Stop a running instance')
-    .action(async (id: string) => {
-      const instance = await client.post<Instance>(`/api/v1/instances/${id}/stop`);
-      log(`Instance ${id} stopped (status: ${instance.status})`);
-    });
-
-  cmd
-    .command('restart <id>')
-    .description('Restart an instance (stop, remove, start fresh)')
-    .action(async (id: string) => {
-      const instance = await client.post<Instance>(`/api/v1/instances/${id}/restart`);
-      log(`Instance restarted as ${instance.id} (status: ${instance.status})`);
-    });
-
-  cmd
-    .command('remove <id>')
-    .alias('rm')
-    .description('Remove an instance and its container')
-    .action(async (id: string) => {
-      await client.delete(`/api/v1/instances/${id}`);
-      log(`Instance ${id} removed.`);
-    });
-
-  cmd
-    .command('logs <id>')
-    .description('Get logs from an instance')
-    .option('-t, --tail <lines>', 'Number of lines to show')
-    .action(async (id: string, opts: { tail?: string }) => {
-      let url = `/api/v1/instances/${id}/logs`;
-      if (opts.tail) {
-        url += `?tail=${opts.tail}`;
-      }
-      const logs = await client.get<{ stdout: string; stderr: string }>(url);
-      if (logs.stdout) {
-        log(logs.stdout);
-      }
-      if (logs.stderr) {
-        process.stderr.write(logs.stderr);
-      }
-    });
-
-  cmd
-    .command('inspect <id>')
-    .description('Get detailed container info for an instance')
-    .action(async (id: string) => {
-      const info = await client.get(`/api/v1/instances/${id}/inspect`);
-      log(JSON.stringify(info, null, 2));
-    });
-
-  return cmd;
-}

src/cli/src/commands/logs.ts

@@ -0,0 +1,29 @@
+import { Command } from 'commander';
+import type { ApiClient } from '../api-client.js';
+
+export interface LogsCommandDeps {
+  client: ApiClient;
+  log: (...args: unknown[]) => void;
+}
+
+export function createLogsCommand(deps: LogsCommandDeps): Command {
+  const { client, log } = deps;
+
+  return new Command('logs')
+    .description('Get logs from an MCP server instance')
+    .argument('<instance-id>', 'Instance ID')
+    .option('-t, --tail <lines>', 'Number of lines to show')
+    .action(async (id: string, opts: { tail?: string }) => {
+      let url = `/api/v1/instances/${id}/logs`;
+      if (opts.tail) {
+        url += `?tail=${opts.tail}`;
+      }
+      const logs = await client.get<{ stdout: string; stderr: string }>(url);
+      if (logs.stdout) {
+        log(logs.stdout);
+      }
+      if (logs.stderr) {
+        process.stderr.write(logs.stderr);
+      }
+    });
+}

src/cli/src/commands/project.ts

@@ -1,129 +1,15 @@
 import { Command } from 'commander';
 import type { ApiClient } from '../api-client.js';
 
-interface Project {
-  id: string;
-  name: string;
-  description: string;
-  ownerId: string;
-  createdAt: string;
-}
-
-interface Profile {
-  id: string;
-  name: string;
-  serverId: string;
-}
-
 export interface ProjectCommandDeps {
   client: ApiClient;
   log: (...args: unknown[]) => void;
 }
 
 export function createProjectCommand(deps: ProjectCommandDeps): Command {
-  const { client, log } = deps;
-
   const cmd = new Command('project')
-    .alias('projects')
     .alias('proj')
-    .description('Manage mcpctl projects');
-
-  cmd
-    .command('list')
-    .alias('ls')
-    .description('List all projects')
-    .option('-o, --output <format>', 'Output format (table, json)', 'table')
-    .action(async (opts: { output: string }) => {
-      const projects = await client.get<Project[]>('/api/v1/projects');
-      if (opts.output === 'json') {
-        log(JSON.stringify(projects, null, 2));
-        return;
-      }
-      if (projects.length === 0) {
-        log('No projects found.');
-        return;
-      }
-      log('ID\tNAME\tDESCRIPTION');
-      for (const p of projects) {
-        log(`${p.id}\t${p.name}\t${p.description || '-'}`);
-      }
-    });
-
-  cmd
-    .command('create <name>')
-    .description('Create a new project')
-    .option('-d, --description <text>', 'Project description', '')
-    .action(async (name: string, opts: { description: string }) => {
-      const project = await client.post<Project>('/api/v1/projects', {
-        name,
-        description: opts.description,
-      });
-      log(`Project '${project.name}' created (id: ${project.id})`);
-    });
-
-  cmd
-    .command('delete <id>')
-    .alias('rm')
-    .description('Delete a project')
-    .action(async (id: string) => {
-      await client.delete(`/api/v1/projects/${id}`);
-      log(`Project '${id}' deleted.`);
-    });
-
-  cmd
-    .command('show <id>')
-    .description('Show project details')
-    .action(async (id: string) => {
-      const project = await client.get<Project>(`/api/v1/projects/${id}`);
-      log(`Name: ${project.name}`);
-      log(`ID: ${project.id}`);
-      log(`Description: ${project.description || '-'}`);
-      log(`Owner: ${project.ownerId}`);
-      log(`Created: ${project.createdAt}`);
-
-      try {
-        const profiles = await client.get<Profile[]>(`/api/v1/projects/${id}/profiles`);
-        if (profiles.length > 0) {
-          log('\nProfiles:');
-          for (const p of profiles) {
-            log(`  - ${p.name} (id: ${p.id})`);
-          }
-        } else {
-          log('\nNo profiles assigned.');
-        }
-      } catch {
-        // Profiles endpoint may not be available
-      }
-    });
-
-  cmd
-    .command('profiles <id>')
-    .description('List profiles assigned to a project')
-    .option('-o, --output <format>', 'Output format (table, json)', 'table')
-    .action(async (id: string, opts: { output: string }) => {
-      const profiles = await client.get<Profile[]>(`/api/v1/projects/${id}/profiles`);
-      if (opts.output === 'json') {
-        log(JSON.stringify(profiles, null, 2));
-        return;
-      }
-      if (profiles.length === 0) {
-        log('No profiles assigned.');
-        return;
-      }
-      log('ID\tNAME\tSERVER');
-      for (const p of profiles) {
-        log(`${p.id}\t${p.name}\t${p.serverId}`);
-      }
-    });
-
-  cmd
-    .command('set-profiles <id>')
-    .description('Set the profiles assigned to a project')
-    .argument('<profileIds...>', 'Profile IDs to assign')
-    .action(async (id: string, profileIds: string[]) => {
-      await client.put(`/api/v1/projects/${id}/profiles`, { profileIds });
-      log(`Set ${profileIds.length} profile(s) for project '${id}'.`);
-    });
+    .description('Project-specific actions (create with "create project", list with "get projects")');
 
   return cmd;
 }

src/cli/src/commands/setup.ts

@@ -1,103 +0,0 @@
-import { Command } from 'commander';
-import type { ApiClient } from '../api-client.js';
-
-export interface SetupPromptDeps {
-  input: (message: string) => Promise<string>;
-  password: (message: string) => Promise<string>;
-  select: <T extends string>(message: string, choices: Array<{ name: string; value: T }>) => Promise<T>;
-  confirm: (message: string) => Promise<boolean>;
-}
-
-export interface SetupCommandDeps {
-  client: ApiClient;
-  prompt: SetupPromptDeps;
-  log: (...args: unknown[]) => void;
-}
-
-export function createSetupCommand(deps: SetupCommandDeps): Command {
-  const { client, prompt, log } = deps;
-
-  return new Command('setup')
-    .description('Interactive wizard for configuring an MCP server')
-    .argument('[server-name]', 'Server name to set up (will prompt if not given)')
-    .action(async (serverName?: string) => {
-      log('MCP Server Setup Wizard\n');
-
-      // Step 1: Server name
-      const name = serverName ?? await prompt.input('Server name (lowercase, hyphens allowed):');
-      if (!name) {
-        log('Setup cancelled.');
-        return;
-      }
-
-      // Step 2: Transport
-      const transport = await prompt.select('Transport type:', [
-        { name: 'STDIO (command-line process)', value: 'STDIO' as const },
-        { name: 'SSE (Server-Sent Events over HTTP)', value: 'SSE' as const },
-        { name: 'Streamable HTTP', value: 'STREAMABLE_HTTP' as const },
-      ]);
-
-      // Step 3: Package or image
-      const packageName = await prompt.input('NPM package name (or leave empty):');
-      const dockerImage = await prompt.input('Docker image (or leave empty):');
-
-      // Step 4: Description
-      const description = await prompt.input('Description:');
-
-      // Step 5: Create the server
-      const serverData: Record<string, unknown> = {
-        name,
-        transport,
-        description,
-      };
-      if (packageName) serverData.packageName = packageName;
-      if (dockerImage) serverData.dockerImage = dockerImage;
-
-      let server: { id: string; name: string };
-      try {
-        server = await client.post<{ id: string; name: string }>('/api/v1/servers', serverData);
-        log(`\nServer '${server.name}' created.`);
-      } catch (err) {
-        log(`\nFailed to create server: ${err instanceof Error ? err.message : err}`);
-        return;
-      }
-
-      // Step 6: Create a profile with env vars
-      const createProfile = await prompt.confirm('Create a profile with environment variables?');
-      if (!createProfile) {
-        log('\nSetup complete!');
-        return;
-      }
-
-      const profileName = await prompt.input('Profile name:') || 'default';
-
-      // Collect env vars
-      const envOverrides: Record<string, string> = {};
-      let addMore = true;
-      while (addMore) {
-        const envName = await prompt.input('Environment variable name (empty to finish):');
-        if (!envName) break;
-
-        const isSecret = await prompt.confirm(`Is '${envName}' a secret (e.g., API key)?`);
-        const envValue = isSecret
-          ? await prompt.password(`Value for ${envName}:`)
-          : await prompt.input(`Value for ${envName}:`);
-
-        envOverrides[envName] = envValue;
-        addMore = await prompt.confirm('Add another environment variable?');
-      }
-
-      try {
-        await client.post('/api/v1/profiles', {
-          name: profileName,
-          serverId: server.id,
-          envOverrides,
-        });
-        log(`Profile '${profileName}' created for server '${name}'.`);
-      } catch (err) {
-        log(`Failed to create profile: ${err instanceof Error ? err.message : err}`);
-      }
-
-      log('\nSetup complete!');
-    });
-}

src/cli/src/commands/shared.ts

@@ -0,0 +1,42 @@
+import type { ApiClient } from '../api-client.js';
+
+export const RESOURCE_ALIASES: Record<string, string> = {
+  server: 'servers',
+  srv: 'servers',
+  project: 'projects',
+  proj: 'projects',
+  instance: 'instances',
+  inst: 'instances',
+  secret: 'secrets',
+  sec: 'secrets',
+};
+
+export function resolveResource(name: string): string {
+  const lower = name.toLowerCase();
+  return RESOURCE_ALIASES[lower] ?? lower;
+}
+
+/** Resolve a name-or-ID to an ID. CUIDs pass through; names are looked up. */
+export async function resolveNameOrId(
+  client: ApiClient,
+  resource: string,
+  nameOrId: string,
+): Promise<string> {
+  // CUIDs start with 'c' followed by 24+ alphanumeric chars
+  if (/^c[a-z0-9]{24}/.test(nameOrId)) {
+    return nameOrId;
+  }
+  const items = await client.get<Array<{ id: string; name: string }>>(`/api/v1/${resource}`);
+  const match = items.find((item) => item.name === nameOrId);
+  if (match) return match.id;
+  throw new Error(`${resource.replace(/s$/, '')} '${nameOrId}' not found`);
+}
+
+/** Strip internal/read-only fields from an API response to make it apply-compatible. */
+export function stripInternalFields(obj: Record<string, unknown>): Record<string, unknown> {
+  const result = { ...obj };
+  for (const key of ['id', 'createdAt', 'updatedAt', 'version', 'ownerId']) {
+    delete result[key];
+  }
+  return result;
+}

src/cli/src/index.ts

@@ -5,9 +5,11 @@ import { createConfigCommand } from './commands/config.js';
 import { createStatusCommand } from './commands/status.js';
 import { createGetCommand } from './commands/get.js';
 import { createDescribeCommand } from './commands/describe.js';
-import { createInstanceCommands } from './commands/instances.js';
+import { createDeleteCommand } from './commands/delete.js';
+import { createLogsCommand } from './commands/logs.js';
 import { createApplyCommand } from './commands/apply.js';
-import { createSetupCommand } from './commands/setup.js';
+import { createCreateCommand } from './commands/create.js';
+import { createEditCommand } from './commands/edit.js';
 import { createClaudeCommand } from './commands/claude.js';
 import { createProjectCommand } from './commands/project.js';
 import { createBackupCommand, createRestoreCommand } from './commands/backup.js';
@@ -15,13 +17,14 @@ import { createLoginCommand, createLogoutCommand } from './commands/auth.js';
 import { ApiClient } from './api-client.js';
 import { loadConfig } from './config/index.js';
 import { loadCredentials } from './auth/index.js';
+import { resolveNameOrId } from './commands/shared.js';
 
 export function createProgram(): Command {
   const program = new Command()
     .name(APP_NAME)
     .description('Manage MCP servers like kubectl manages containers')
     .version(APP_VERSION, '-v, --version')
-    .option('-o, --output <format>', 'output format (table, json, yaml)', 'table')
+    .enablePositionalOptions()
     .option('--daemon-url <url>', 'mcplocal daemon URL')
     .option('--direct', 'bypass mcplocal and connect directly to mcpd');
 
@@ -45,15 +48,27 @@ export function createProgram(): Command {
 
   const client = new ApiClient({ baseUrl, token: creds?.token ?? undefined });
 
-  const fetchResource = async (resource: string, id?: string): Promise<unknown[]> => {
-    if (id) {
+  const fetchResource = async (resource: string, nameOrId?: string): Promise<unknown[]> => {
+    if (nameOrId) {
+      let id: string;
+      try {
+        id = await resolveNameOrId(client, resource, nameOrId);
+      } catch {
+        id = nameOrId;
+      }
       const item = await client.get(`/api/v1/${resource}/${id}`);
       return [item];
     }
     return client.get<unknown[]>(`/api/v1/${resource}`);
   };
 
-  const fetchSingleResource = async (resource: string, id: string): Promise<unknown> => {
+  const fetchSingleResource = async (resource: string, nameOrId: string): Promise<unknown> => {
+    let id: string;
+    try {
+      id = await resolveNameOrId(client, resource, nameOrId);
+    } catch {
+      id = nameOrId;
+    }
     return client.get(`/api/v1/${resource}/${id}`);
   };
 
@@ -63,11 +78,28 @@ export function createProgram(): Command {
   }));
 
   program.addCommand(createDescribeCommand({
+    client,
     fetchResource: fetchSingleResource,
+    fetchInspect: async (id: string) => client.get(`/api/v1/instances/${id}/inspect`),
     log: (...args) => console.log(...args),
   }));
 
-  program.addCommand(createInstanceCommands({
+  program.addCommand(createDeleteCommand({
+    client,
+    log: (...args) => console.log(...args),
+  }));
+
+  program.addCommand(createLogsCommand({
+    client,
+    log: (...args) => console.log(...args),
+  }));
+
+  program.addCommand(createCreateCommand({
+    client,
+    log: (...args) => console.log(...args),
+  }));
+
+  program.addCommand(createEditCommand({
     client,
     log: (...args) => console.log(...args),
   }));
@@ -77,33 +109,6 @@ export function createProgram(): Command {
     log: (...args) => console.log(...args),
   }));
 
-  program.addCommand(createSetupCommand({
-    client,
-    prompt: {
-      async input(message) {
-        const { default: inquirer } = await import('inquirer');
-        const { answer } = await inquirer.prompt([{ type: 'input', name: 'answer', message }]);
-        return answer as string;
-      },
-      async password(message) {
-        const { default: inquirer } = await import('inquirer');
-        const { answer } = await inquirer.prompt([{ type: 'password', name: 'answer', message }]);
-        return answer as string;
-      },
-      async select(message, choices) {
-        const { default: inquirer } = await import('inquirer');
-        const { answer } = await inquirer.prompt([{ type: 'list', name: 'answer', message, choices }]);
-        return answer;
-      },
-      async confirm(message) {
-        const { default: inquirer } = await import('inquirer');
-        const { answer } = await inquirer.prompt([{ type: 'confirm', name: 'answer', message }]);
-        return answer as boolean;
-      },
-    },
-    log: (...args) => console.log(...args),
-  }));
-
   program.addCommand(createClaudeCommand({
     client,
     log: (...args) => console.log(...args),

src/cli/tests/cli.test.ts

@@ -24,9 +24,10 @@ describe('createProgram', () => {
     expect(status).toBeDefined();
   });
 
-  it('has output option', () => {
+  it('subcommands have output option', () => {
     const program = createProgram();
-    const opt = program.options.find((o) => o.long === '--output');
+    const get = program.commands.find((c) => c.name() === 'get');
+    const opt = get?.options.find((o) => o.long === '--output');
     expect(opt).toBeDefined();
   });
 

src/cli/tests/commands/apply.test.ts

@@ -86,9 +86,6 @@ servers:
 servers:
   - name: test
     transport: STDIO
-profiles:
-  - name: default
-    server: test
 `);
 
     const cmd = createApplyCommand({ client, log });
@@ -97,52 +94,51 @@ profiles:
     expect(client.post).not.toHaveBeenCalled();
     expect(output.join('\n')).toContain('Dry run');
     expect(output.join('\n')).toContain('1 server(s)');
-    expect(output.join('\n')).toContain('1 profile(s)');
 
     rmSync(tmpDir, { recursive: true, force: true });
   });
 
-  it('applies profiles with server lookup', async () => {
+  it('applies secrets', async () => {
+    const configPath = join(tmpDir, 'config.yaml');
+    writeFileSync(configPath, `
+secrets:
+  - name: ha-creds
+    data:
+      TOKEN: abc123
+      URL: https://ha.local
+`);
+
+    const cmd = createApplyCommand({ client, log });
+    await cmd.parseAsync([configPath], { from: 'user' });
+
+    expect(client.post).toHaveBeenCalledWith('/api/v1/secrets', expect.objectContaining({
+      name: 'ha-creds',
+      data: { TOKEN: 'abc123', URL: 'https://ha.local' },
+    }));
+    expect(output.join('\n')).toContain('Created secret: ha-creds');
+
+    rmSync(tmpDir, { recursive: true, force: true });
+  });
+
+  it('updates existing secrets', async () => {
     vi.mocked(client.get).mockImplementation(async (url: string) => {
-      if (url === '/api/v1/servers') return [{ id: 'srv-1', name: 'slack' }];
+      if (url === '/api/v1/secrets') return [{ id: 'sec-1', name: 'ha-creds' }];
       return [];
     });
 
     const configPath = join(tmpDir, 'config.yaml');
     writeFileSync(configPath, `
-profiles:
-  - name: default
-    server: slack
-    envOverrides:
-      SLACK_TOKEN: "xoxb-test"
+secrets:
+  - name: ha-creds
+    data:
+      TOKEN: new-token
 `);
 
     const cmd = createApplyCommand({ client, log });
     await cmd.parseAsync([configPath], { from: 'user' });
 
-    expect(client.post).toHaveBeenCalledWith('/api/v1/profiles', expect.objectContaining({
-      name: 'default',
-      serverId: 'srv-1',
-      envOverrides: { SLACK_TOKEN: 'xoxb-test' },
-    }));
-    expect(output.join('\n')).toContain('Created profile: default');
-
-    rmSync(tmpDir, { recursive: true, force: true });
-  });
-
-  it('skips profiles when server not found', async () => {
-    const configPath = join(tmpDir, 'config.yaml');
-    writeFileSync(configPath, `
-profiles:
-  - name: default
-    server: nonexistent
-`);
-
-    const cmd = createApplyCommand({ client, log });
-    await cmd.parseAsync([configPath], { from: 'user' });
-
-    expect(client.post).not.toHaveBeenCalled();
-    expect(output.join('\n')).toContain("Skipping profile 'default'");
+    expect(client.put).toHaveBeenCalledWith('/api/v1/secrets/sec-1', { data: { TOKEN: 'new-token' } });
+    expect(output.join('\n')).toContain('Updated secret: ha-creds');
 
     rmSync(tmpDir, { recursive: true, force: true });
   });

src/cli/tests/commands/create.test.ts

@@ -0,0 +1,123 @@
+import { describe, it, expect, vi, beforeEach } from 'vitest';
+import { createCreateCommand } from '../../src/commands/create.js';
+import type { ApiClient } from '../../src/api-client.js';
+
+function mockClient(): ApiClient {
+  return {
+    get: vi.fn(async () => []),
+    post: vi.fn(async () => ({ id: 'new-id', name: 'test' })),
+    put: vi.fn(async () => ({})),
+    delete: vi.fn(async () => {}),
+  } as unknown as ApiClient;
+}
+
+describe('create command', () => {
+  let client: ReturnType<typeof mockClient>;
+  let output: string[];
+  const log = (...args: unknown[]) => output.push(args.map(String).join(' '));
+
+  beforeEach(() => {
+    client = mockClient();
+    output = [];
+  });
+
+  describe('create server', () => {
+    it('creates a server with minimal flags', async () => {
+      const cmd = createCreateCommand({ client, log });
+      await cmd.parseAsync(['server', 'my-server'], { from: 'user' });
+      expect(client.post).toHaveBeenCalledWith('/api/v1/servers', expect.objectContaining({
+        name: 'my-server',
+        transport: 'STDIO',
+        replicas: 1,
+      }));
+      expect(output.join('\n')).toContain("server 'test' created");
+    });
+
+    it('creates a server with all flags', async () => {
+      const cmd = createCreateCommand({ client, log });
+      await cmd.parseAsync([
+        'server', 'ha-mcp',
+        '-d', 'Home Assistant MCP',
+        '--docker-image', 'ghcr.io/ha-mcp:latest',
+        '--transport', 'STREAMABLE_HTTP',
+        '--external-url', 'http://localhost:8086/mcp',
+        '--container-port', '3000',
+        '--replicas', '2',
+        '--command', 'python',
+        '--command', '-c',
+        '--command', 'print("hello")',
+        '--env', 'API_KEY=secretRef:creds:API_KEY',
+        '--env', 'BASE_URL=http://localhost',
+      ], { from: 'user' });
+
+      expect(client.post).toHaveBeenCalledWith('/api/v1/servers', {
+        name: 'ha-mcp',
+        description: 'Home Assistant MCP',
+        dockerImage: 'ghcr.io/ha-mcp:latest',
+        transport: 'STREAMABLE_HTTP',
+        externalUrl: 'http://localhost:8086/mcp',
+        containerPort: 3000,
+        replicas: 2,
+        command: ['python', '-c', 'print("hello")'],
+        env: [
+          { name: 'API_KEY', valueFrom: { secretRef: { name: 'creds', key: 'API_KEY' } } },
+          { name: 'BASE_URL', value: 'http://localhost' },
+        ],
+      });
+    });
+
+    it('defaults transport to STDIO', async () => {
+      const cmd = createCreateCommand({ client, log });
+      await cmd.parseAsync(['server', 'test'], { from: 'user' });
+      expect(client.post).toHaveBeenCalledWith('/api/v1/servers', expect.objectContaining({
+        transport: 'STDIO',
+      }));
+    });
+  });
+
+  describe('create secret', () => {
+    it('creates a secret with --data flags', async () => {
+      const cmd = createCreateCommand({ client, log });
+      await cmd.parseAsync([
+        'secret', 'ha-creds',
+        '--data', 'TOKEN=abc123',
+        '--data', 'URL=https://ha.local',
+      ], { from: 'user' });
+      expect(client.post).toHaveBeenCalledWith('/api/v1/secrets', {
+        name: 'ha-creds',
+        data: { TOKEN: 'abc123', URL: 'https://ha.local' },
+      });
+      expect(output.join('\n')).toContain("secret 'test' created");
+    });
+
+    it('creates a secret with empty data', async () => {
+      const cmd = createCreateCommand({ client, log });
+      await cmd.parseAsync(['secret', 'empty-secret'], { from: 'user' });
+      expect(client.post).toHaveBeenCalledWith('/api/v1/secrets', {
+        name: 'empty-secret',
+        data: {},
+      });
+    });
+  });
+
+  describe('create project', () => {
+    it('creates a project', async () => {
+      const cmd = createCreateCommand({ client, log });
+      await cmd.parseAsync(['project', 'my-project', '-d', 'A test project'], { from: 'user' });
+      expect(client.post).toHaveBeenCalledWith('/api/v1/projects', {
+        name: 'my-project',
+        description: 'A test project',
+      });
+      expect(output.join('\n')).toContain("project 'test' created");
+    });
+
+    it('creates a project with no description', async () => {
+      const cmd = createCreateCommand({ client, log });
+      await cmd.parseAsync(['project', 'minimal'], { from: 'user' });
+      expect(client.post).toHaveBeenCalledWith('/api/v1/projects', {
+        name: 'minimal',
+        description: '',
+      });
+    });
+  });
+});

src/cli/tests/commands/describe.test.ts

@@ -1,42 +1,59 @@
 import { describe, it, expect, vi } from 'vitest';
 import { createDescribeCommand } from '../../src/commands/describe.js';
 import type { DescribeCommandDeps } from '../../src/commands/describe.js';
+import type { ApiClient } from '../../src/api-client.js';
+
+function mockClient(): ApiClient {
+  return {
+    get: vi.fn(async () => []),
+    post: vi.fn(async () => ({})),
+    put: vi.fn(async () => ({})),
+    delete: vi.fn(async () => {}),
+  } as unknown as ApiClient;
+}
 
 function makeDeps(item: unknown = {}): DescribeCommandDeps & { output: string[] } {
   const output: string[] = [];
   return {
     output,
+    client: mockClient(),
     fetchResource: vi.fn(async () => item),
     log: (...args: string[]) => output.push(args.join(' ')),
   };
 }
 
 describe('describe command', () => {
-  it('shows detailed server info', async () => {
+  it('shows detailed server info with sections', async () => {
     const deps = makeDeps({
       id: 'srv-1',
       name: 'slack',
       transport: 'STDIO',
       packageName: '@slack/mcp',
       dockerImage: null,
-      envTemplate: [],
+      env: [],
+      createdAt: '2025-01-01',
     });
     const cmd = createDescribeCommand(deps);
     await cmd.parseAsync(['node', 'test', 'server', 'srv-1']);
 
     expect(deps.fetchResource).toHaveBeenCalledWith('servers', 'srv-1');
     const text = deps.output.join('\n');
-    expect(text).toContain('--- Server ---');
-    expect(text).toContain('name: slack');
-    expect(text).toContain('transport: STDIO');
-    expect(text).toContain('dockerImage: -');
+    expect(text).toContain('=== Server: slack ===');
+    expect(text).toContain('Name:');
+    expect(text).toContain('slack');
+    expect(text).toContain('Transport:');
+    expect(text).toContain('STDIO');
+    expect(text).toContain('Package:');
+    expect(text).toContain('@slack/mcp');
+    expect(text).toContain('Metadata:');
+    expect(text).toContain('ID:');
   });
 
   it('resolves resource aliases', async () => {
-    const deps = makeDeps({ id: 'p1' });
+    const deps = makeDeps({ id: 's1' });
     const cmd = createDescribeCommand(deps);
-    await cmd.parseAsync(['node', 'test', 'prof', 'p1']);
-    expect(deps.fetchResource).toHaveBeenCalledWith('profiles', 'p1');
+    await cmd.parseAsync(['node', 'test', 'sec', 's1']);
+    expect(deps.fetchResource).toHaveBeenCalledWith('secrets', 's1');
   });
 
   it('outputs JSON format', async () => {
@@ -55,31 +72,71 @@ describe('describe command', () => {
     expect(deps.output[0]).toContain('name: slack');
   });
 
-  it('formats nested objects', async () => {
+  it('shows project detail', async () => {
     const deps = makeDeps({
-      id: 'srv-1',
-      name: 'slack',
-      metadata: { version: '1.0', nested: { deep: true } },
+      id: 'proj-1',
+      name: 'my-project',
+      description: 'A test project',
+      ownerId: 'user-1',
+      createdAt: '2025-01-01',
     });
     const cmd = createDescribeCommand(deps);
-    await cmd.parseAsync(['node', 'test', 'server', 'srv-1']);
+    await cmd.parseAsync(['node', 'test', 'project', 'proj-1']);
 
     const text = deps.output.join('\n');
-    expect(text).toContain('metadata:');
-    expect(text).toContain('version: 1.0');
+    expect(text).toContain('=== Project: my-project ===');
+    expect(text).toContain('A test project');
+    expect(text).toContain('user-1');
   });
 
-  it('formats arrays correctly', async () => {
+  it('shows secret detail with masked values', async () => {
     const deps = makeDeps({
-      id: 'srv-1',
-      permissions: ['read', 'write'],
-      envTemplate: [],
+      id: 'sec-1',
+      name: 'ha-creds',
+      data: { TOKEN: 'abc123', URL: 'https://ha.local' },
+      createdAt: '2025-01-01',
     });
     const cmd = createDescribeCommand(deps);
-    await cmd.parseAsync(['node', 'test', 'server', 'srv-1']);
+    await cmd.parseAsync(['node', 'test', 'secret', 'sec-1']);
 
     const text = deps.output.join('\n');
-    expect(text).toContain('permissions: read, write');
-    expect(text).toContain('envTemplate: []');
+    expect(text).toContain('=== Secret: ha-creds ===');
+    expect(text).toContain('TOKEN');
+    expect(text).toContain('***');
+    expect(text).not.toContain('abc123');
+    expect(text).toContain('use --show-values to reveal');
+  });
+
+  it('shows secret detail with revealed values when --show-values', async () => {
+    const deps = makeDeps({
+      id: 'sec-1',
+      name: 'ha-creds',
+      data: { TOKEN: 'abc123' },
+      createdAt: '2025-01-01',
+    });
+    const cmd = createDescribeCommand(deps);
+    await cmd.parseAsync(['node', 'test', 'secret', 'sec-1', '--show-values']);
+
+    const text = deps.output.join('\n');
+    expect(text).toContain('abc123');
+    expect(text).not.toContain('***');
+  });
+
+  it('shows instance detail with container info', async () => {
+    const deps = makeDeps({
+      id: 'inst-1',
+      serverId: 'srv-1',
+      status: 'RUNNING',
+      containerId: 'abc123',
+      port: 3000,
+      createdAt: '2025-01-01',
+    });
+    const cmd = createDescribeCommand(deps);
+    await cmd.parseAsync(['node', 'test', 'instance', 'inst-1']);
+
+    const text = deps.output.join('\n');
+    expect(text).toContain('=== Instance: inst-1 ===');
+    expect(text).toContain('RUNNING');
+    expect(text).toContain('abc123');
   });
 });

src/cli/tests/commands/edit.test.ts

@@ -0,0 +1,153 @@
+import { describe, it, expect, vi, beforeEach } from 'vitest';
+import { readFileSync, writeFileSync } from 'node:fs';
+import yaml from 'js-yaml';
+import { createEditCommand } from '../../src/commands/edit.js';
+import type { ApiClient } from '../../src/api-client.js';
+
+function mockClient(): ApiClient {
+  return {
+    get: vi.fn(async () => ({})),
+    post: vi.fn(async () => ({})),
+    put: vi.fn(async () => ({})),
+    delete: vi.fn(async () => {}),
+  } as unknown as ApiClient;
+}
+
+describe('edit command', () => {
+  let client: ReturnType<typeof mockClient>;
+  let output: string[];
+  const log = (...args: unknown[]) => output.push(args.map(String).join(' '));
+
+  beforeEach(() => {
+    client = mockClient();
+    output = [];
+  });
+
+  it('fetches server, opens editor, applies changes on save', async () => {
+    // GET /api/v1/servers returns list for resolveNameOrId
+    vi.mocked(client.get).mockImplementation(async (path: string) => {
+      if (path === '/api/v1/servers') {
+        return [{ id: 'srv-1', name: 'ha-mcp' }];
+      }
+      // GET /api/v1/servers/srv-1 returns full server
+      return {
+        id: 'srv-1',
+        name: 'ha-mcp',
+        description: 'Old desc',
+        transport: 'STDIO',
+        replicas: 1,
+        createdAt: '2025-01-01',
+        updatedAt: '2025-01-01',
+        version: 1,
+      };
+    });
+
+    const cmd = createEditCommand({
+      client,
+      log,
+      getEditor: () => 'vi',
+      openEditor: (filePath) => {
+        // Simulate user editing the file
+        const content = readFileSync(filePath, 'utf-8');
+        const modified = content
+          .replace('Old desc', 'New desc')
+          .replace('replicas: 1', 'replicas: 3');
+        writeFileSync(filePath, modified, 'utf-8');
+      },
+    });
+
+    await cmd.parseAsync(['server', 'ha-mcp'], { from: 'user' });
+
+    expect(client.put).toHaveBeenCalledWith('/api/v1/servers/srv-1', expect.objectContaining({
+      description: 'New desc',
+      replicas: 3,
+    }));
+    expect(output.join('\n')).toContain("server 'ha-mcp' updated");
+  });
+
+  it('detects no changes and skips PUT', async () => {
+    vi.mocked(client.get).mockImplementation(async (path: string) => {
+      if (path === '/api/v1/servers') return [{ id: 'srv-1', name: 'test' }];
+      return {
+        id: 'srv-1', name: 'test', description: '', transport: 'STDIO',
+        createdAt: '2025-01-01', updatedAt: '2025-01-01', version: 1,
+      };
+    });
+
+    const cmd = createEditCommand({
+      client,
+      log,
+      getEditor: () => 'vi',
+      openEditor: () => {
+        // Don't modify the file
+      },
+    });
+
+    await cmd.parseAsync(['server', 'test'], { from: 'user' });
+
+    expect(client.put).not.toHaveBeenCalled();
+    expect(output.join('\n')).toContain("unchanged");
+  });
+
+  it('handles empty file as cancel', async () => {
+    vi.mocked(client.get).mockImplementation(async (path: string) => {
+      if (path === '/api/v1/servers') return [{ id: 'srv-1', name: 'test' }];
+      return { id: 'srv-1', name: 'test', createdAt: '2025-01-01', updatedAt: '2025-01-01', version: 1 };
+    });
+
+    const cmd = createEditCommand({
+      client,
+      log,
+      getEditor: () => 'vi',
+      openEditor: (filePath) => {
+        writeFileSync(filePath, '', 'utf-8');
+      },
+    });
+
+    await cmd.parseAsync(['server', 'test'], { from: 'user' });
+
+    expect(client.put).not.toHaveBeenCalled();
+    expect(output.join('\n')).toContain('cancelled');
+  });
+
+  it('strips read-only fields from editor content', async () => {
+    vi.mocked(client.get).mockImplementation(async (path: string) => {
+      if (path === '/api/v1/servers') return [{ id: 'srv-1', name: 'test' }];
+      return {
+        id: 'srv-1', name: 'test', description: '', transport: 'STDIO',
+        createdAt: '2025-01-01', updatedAt: '2025-01-01', version: 1,
+      };
+    });
+
+    let editorContent = '';
+    const cmd = createEditCommand({
+      client,
+      log,
+      getEditor: () => 'vi',
+      openEditor: (filePath) => {
+        editorContent = readFileSync(filePath, 'utf-8');
+      },
+    });
+
+    await cmd.parseAsync(['server', 'test'], { from: 'user' });
+
+    // The editor content should NOT contain read-only fields
+    expect(editorContent).not.toContain('id:');
+    expect(editorContent).not.toContain('createdAt');
+    expect(editorContent).not.toContain('updatedAt');
+    expect(editorContent).not.toContain('version');
+    // But should contain editable fields
+    expect(editorContent).toContain('name:');
+  });
+
+  it('rejects edit instance with error message', async () => {
+    const cmd = createEditCommand({ client, log });
+
+    await cmd.parseAsync(['instance', 'inst-1'], { from: 'user' });
+
+    expect(client.get).not.toHaveBeenCalled();
+    expect(client.put).not.toHaveBeenCalled();
+    expect(output.join('\n')).toContain('immutable');
+  });
+
+});

src/cli/tests/commands/get.test.ts

@@ -41,30 +41,30 @@ describe('get command', () => {
     expect(deps.fetchResource).toHaveBeenCalledWith('servers', 'srv-1');
   });
 
-  it('outputs JSON format', async () => {
-    const deps = makeDeps([{ id: 'srv-1', name: 'slack' }]);
+  it('outputs apply-compatible JSON format', async () => {
+    const deps = makeDeps([{ id: 'srv-1', name: 'slack', createdAt: '2025-01-01', updatedAt: '2025-01-01', version: 1 }]);
     const cmd = createGetCommand(deps);
     await cmd.parseAsync(['node', 'test', 'servers', '-o', 'json']);
 
     const parsed = JSON.parse(deps.output[0] ?? '');
-    expect(parsed).toEqual({ id: 'srv-1', name: 'slack' });
+    // Wrapped in resource key, internal fields stripped
+    expect(parsed).toHaveProperty('servers');
+    expect(parsed.servers[0].name).toBe('slack');
+    expect(parsed.servers[0]).not.toHaveProperty('id');
+    expect(parsed.servers[0]).not.toHaveProperty('createdAt');
+    expect(parsed.servers[0]).not.toHaveProperty('updatedAt');
+    expect(parsed.servers[0]).not.toHaveProperty('version');
   });
 
-  it('outputs YAML format', async () => {
-    const deps = makeDeps([{ id: 'srv-1', name: 'slack' }]);
+  it('outputs apply-compatible YAML format', async () => {
+    const deps = makeDeps([{ id: 'srv-1', name: 'slack', createdAt: '2025-01-01' }]);
     const cmd = createGetCommand(deps);
     await cmd.parseAsync(['node', 'test', 'servers', '-o', 'yaml']);
-    expect(deps.output[0]).toContain('name: slack');
-  });
-
-  it('lists profiles with correct columns', async () => {
-    const deps = makeDeps([
-      { id: 'p1', name: 'default', serverId: 'srv-1' },
-    ]);
-    const cmd = createGetCommand(deps);
-    await cmd.parseAsync(['node', 'test', 'profiles']);
-    expect(deps.output[0]).toContain('NAME');
-    expect(deps.output[0]).toContain('SERVER ID');
+    const text = deps.output[0];
+    expect(text).toContain('servers:');
+    expect(text).toContain('name: slack');
+    expect(text).not.toContain('id:');
+    expect(text).not.toContain('createdAt:');
   });
 
   it('lists instances with correct columns', async () => {
@@ -81,6 +81,6 @@ describe('get command', () => {
     const deps = makeDeps([]);
     const cmd = createGetCommand(deps);
     await cmd.parseAsync(['node', 'test', 'servers']);
-    expect(deps.output[0]).toContain('No results');
+    expect(deps.output[0]).toContain('No servers found');
   });
 });

src/cli/tests/commands/instances.test.ts

@@ -1,5 +1,6 @@
 import { describe, it, expect, vi, beforeEach } from 'vitest';
-import { createInstanceCommands } from '../../src/commands/instances.js';
+import { createDeleteCommand } from '../../src/commands/delete.js';
+import { createLogsCommand } from '../../src/commands/logs.js';
 import type { ApiClient } from '../../src/api-client.js';
 
 function mockClient(): ApiClient {
@@ -11,7 +12,7 @@ function mockClient(): ApiClient {
   } as unknown as ApiClient;
 }
 
-describe('instance commands', () => {
+describe('delete command', () => {
   let client: ReturnType<typeof mockClient>;
   let output: string[];
   const log = (...args: unknown[]) => output.push(args.map(String).join(' '));
@@ -21,107 +22,64 @@ describe('instance commands', () => {
     output = [];
   });
 
-  describe('list', () => {
-    it('shows no instances message when empty', async () => {
-      const cmd = createInstanceCommands({ client, log });
-      await cmd.parseAsync(['list'], { from: 'user' });
-      expect(output.join('\n')).toContain('No instances found');
-    });
-
-    it('shows instance table', async () => {
-      vi.mocked(client.get).mockResolvedValue([
-        { id: 'inst-1', serverId: 'srv-1', status: 'RUNNING', containerId: 'ctr-abc123def', port: 3000, createdAt: '2025-01-01' },
-      ]);
-      const cmd = createInstanceCommands({ client, log });
-      await cmd.parseAsync(['list'], { from: 'user' });
-      expect(output.join('\n')).toContain('inst-1');
-      expect(output.join('\n')).toContain('RUNNING');
-    });
-
-    it('filters by server', async () => {
-      const cmd = createInstanceCommands({ client, log });
-      await cmd.parseAsync(['list', '-s', 'srv-1'], { from: 'user' });
-      expect(client.get).toHaveBeenCalledWith(expect.stringContaining('serverId=srv-1'));
-    });
-
-    it('outputs json', async () => {
-      vi.mocked(client.get).mockResolvedValue([{ id: 'inst-1' }]);
-      const cmd = createInstanceCommands({ client, log });
-      await cmd.parseAsync(['list', '-o', 'json'], { from: 'user' });
-      expect(output[0]).toContain('"id"');
-    });
+  it('deletes an instance by ID', async () => {
+    const cmd = createDeleteCommand({ client, log });
+    await cmd.parseAsync(['instance', 'inst-1'], { from: 'user' });
+    expect(client.delete).toHaveBeenCalledWith('/api/v1/instances/inst-1');
+    expect(output.join('\n')).toContain('deleted');
   });
 
-  describe('start', () => {
-    it('starts an instance', async () => {
-      vi.mocked(client.post).mockResolvedValue({ id: 'inst-new', status: 'RUNNING' });
-      const cmd = createInstanceCommands({ client, log });
-      await cmd.parseAsync(['start', 'srv-1'], { from: 'user' });
-      expect(client.post).toHaveBeenCalledWith('/api/v1/instances', { serverId: 'srv-1' });
-      expect(output.join('\n')).toContain('started');
-    });
-
-    it('passes host port', async () => {
-      vi.mocked(client.post).mockResolvedValue({ id: 'inst-new', status: 'RUNNING' });
-      const cmd = createInstanceCommands({ client, log });
-      await cmd.parseAsync(['start', 'srv-1', '-p', '8080'], { from: 'user' });
-      expect(client.post).toHaveBeenCalledWith('/api/v1/instances', { serverId: 'srv-1', hostPort: 8080 });
-    });
+  it('deletes a server by ID', async () => {
+    const cmd = createDeleteCommand({ client, log });
+    await cmd.parseAsync(['server', 'srv-1'], { from: 'user' });
+    expect(client.delete).toHaveBeenCalledWith('/api/v1/servers/srv-1');
+    expect(output.join('\n')).toContain('deleted');
   });
 
-  describe('stop', () => {
-    it('stops an instance', async () => {
-      vi.mocked(client.post).mockResolvedValue({ id: 'inst-1', status: 'STOPPED' });
-      const cmd = createInstanceCommands({ client, log });
-      await cmd.parseAsync(['stop', 'inst-1'], { from: 'user' });
-      expect(client.post).toHaveBeenCalledWith('/api/v1/instances/inst-1/stop');
-      expect(output.join('\n')).toContain('stopped');
-    });
+  it('resolves server name to ID', async () => {
+    vi.mocked(client.get).mockResolvedValue([
+      { id: 'srv-abc', name: 'ha-mcp' },
+    ]);
+    const cmd = createDeleteCommand({ client, log });
+    await cmd.parseAsync(['server', 'ha-mcp'], { from: 'user' });
+    expect(client.delete).toHaveBeenCalledWith('/api/v1/servers/srv-abc');
   });
 
-  describe('restart', () => {
-    it('restarts an instance', async () => {
-      vi.mocked(client.post).mockResolvedValue({ id: 'inst-2', status: 'RUNNING' });
-      const cmd = createInstanceCommands({ client, log });
-      await cmd.parseAsync(['restart', 'inst-1'], { from: 'user' });
-      expect(client.post).toHaveBeenCalledWith('/api/v1/instances/inst-1/restart');
-      expect(output.join('\n')).toContain('restarted');
-    });
+  it('deletes a project', async () => {
+    const cmd = createDeleteCommand({ client, log });
+    await cmd.parseAsync(['project', 'proj-1'], { from: 'user' });
+    expect(client.delete).toHaveBeenCalledWith('/api/v1/projects/proj-1');
   });
 
-  describe('remove', () => {
-    it('removes an instance', async () => {
-      const cmd = createInstanceCommands({ client, log });
-      await cmd.parseAsync(['remove', 'inst-1'], { from: 'user' });
-      expect(client.delete).toHaveBeenCalledWith('/api/v1/instances/inst-1');
-      expect(output.join('\n')).toContain('removed');
-    });
-  });
-
-  describe('logs', () => {
-    it('shows logs', async () => {
-      vi.mocked(client.get).mockResolvedValue({ stdout: 'hello world\n', stderr: '' });
-      const cmd = createInstanceCommands({ client, log });
-      await cmd.parseAsync(['logs', 'inst-1'], { from: 'user' });
-      expect(client.get).toHaveBeenCalledWith('/api/v1/instances/inst-1/logs');
-      expect(output.join('\n')).toContain('hello world');
-    });
-
-    it('passes tail option', async () => {
-      vi.mocked(client.get).mockResolvedValue({ stdout: '', stderr: '' });
-      const cmd = createInstanceCommands({ client, log });
-      await cmd.parseAsync(['logs', 'inst-1', '-t', '50'], { from: 'user' });
-      expect(client.get).toHaveBeenCalledWith('/api/v1/instances/inst-1/logs?tail=50');
-    });
-  });
-
-  describe('inspect', () => {
-    it('shows container info as json', async () => {
-      vi.mocked(client.get).mockResolvedValue({ containerId: 'ctr-abc', state: 'running' });
-      const cmd = createInstanceCommands({ client, log });
-      await cmd.parseAsync(['inspect', 'inst-1'], { from: 'user' });
-      expect(client.get).toHaveBeenCalledWith('/api/v1/instances/inst-1/inspect');
-      expect(output[0]).toContain('ctr-abc');
-    });
+  it('accepts resource aliases', async () => {
+    const cmd = createDeleteCommand({ client, log });
+    await cmd.parseAsync(['srv', 'srv-1'], { from: 'user' });
+    expect(client.delete).toHaveBeenCalledWith('/api/v1/servers/srv-1');
+  });
+});
+
+describe('logs command', () => {
+  let client: ReturnType<typeof mockClient>;
+  let output: string[];
+  const log = (...args: unknown[]) => output.push(args.map(String).join(' '));
+
+  beforeEach(() => {
+    client = mockClient();
+    output = [];
+  });
+
+  it('shows logs', async () => {
+    vi.mocked(client.get).mockResolvedValue({ stdout: 'hello world\n', stderr: '' });
+    const cmd = createLogsCommand({ client, log });
+    await cmd.parseAsync(['inst-1'], { from: 'user' });
+    expect(client.get).toHaveBeenCalledWith('/api/v1/instances/inst-1/logs');
+    expect(output.join('\n')).toContain('hello world');
+  });
+
+  it('passes tail option', async () => {
+    vi.mocked(client.get).mockResolvedValue({ stdout: '', stderr: '' });
+    const cmd = createLogsCommand({ client, log });
+    await cmd.parseAsync(['inst-1', '-t', '50'], { from: 'user' });
+    expect(client.get).toHaveBeenCalledWith('/api/v1/instances/inst-1/logs?tail=50');
   });
 });

src/cli/tests/commands/project.test.ts

@@ -21,91 +21,9 @@ describe('project command', () => {
     output = [];
   });
 
-  describe('list', () => {
-    it('shows no projects message when empty', async () => {
-      const cmd = createProjectCommand({ client, log });
-      await cmd.parseAsync(['list'], { from: 'user' });
-      expect(output.join('\n')).toContain('No projects found');
-    });
-
-    it('shows project table', async () => {
-      vi.mocked(client.get).mockResolvedValue([
-        { id: 'proj-1', name: 'dev', description: 'Dev project', ownerId: 'user-1', createdAt: '2025-01-01' },
-      ]);
-      const cmd = createProjectCommand({ client, log });
-      await cmd.parseAsync(['list'], { from: 'user' });
-      expect(output.join('\n')).toContain('proj-1');
-      expect(output.join('\n')).toContain('dev');
-    });
-
-    it('outputs json', async () => {
-      vi.mocked(client.get).mockResolvedValue([{ id: 'proj-1', name: 'dev' }]);
-      const cmd = createProjectCommand({ client, log });
-      await cmd.parseAsync(['list', '-o', 'json'], { from: 'user' });
-      expect(output[0]).toContain('"id"');
-    });
-  });
-
-  describe('create', () => {
-    it('creates a project', async () => {
-      const cmd = createProjectCommand({ client, log });
-      await cmd.parseAsync(['create', 'my-project', '-d', 'A test project'], { from: 'user' });
-      expect(client.post).toHaveBeenCalledWith('/api/v1/projects', {
-        name: 'my-project',
-        description: 'A test project',
-      });
-      expect(output.join('\n')).toContain("Project 'my-project' created");
-    });
-  });
-
-  describe('delete', () => {
-    it('deletes a project', async () => {
-      const cmd = createProjectCommand({ client, log });
-      await cmd.parseAsync(['delete', 'proj-1'], { from: 'user' });
-      expect(client.delete).toHaveBeenCalledWith('/api/v1/projects/proj-1');
-      expect(output.join('\n')).toContain('deleted');
-    });
-  });
-
-  describe('show', () => {
-    it('shows project details', async () => {
-      vi.mocked(client.get).mockImplementation(async (url: string) => {
-        if (url.endsWith('/profiles')) return [];
-        return { id: 'proj-1', name: 'dev', description: 'Dev project', ownerId: 'user-1', createdAt: '2025-01-01' };
-      });
-      const cmd = createProjectCommand({ client, log });
-      await cmd.parseAsync(['show', 'proj-1'], { from: 'user' });
-      expect(output.join('\n')).toContain('Name: dev');
-      expect(output.join('\n')).toContain('ID: proj-1');
-    });
-  });
-
-  describe('profiles', () => {
-    it('lists profiles for a project', async () => {
-      vi.mocked(client.get).mockResolvedValue([
-        { id: 'prof-1', name: 'default', serverId: 'srv-1' },
-      ]);
-      const cmd = createProjectCommand({ client, log });
-      await cmd.parseAsync(['profiles', 'proj-1'], { from: 'user' });
-      expect(client.get).toHaveBeenCalledWith('/api/v1/projects/proj-1/profiles');
-      expect(output.join('\n')).toContain('default');
-    });
-
-    it('shows empty message when no profiles', async () => {
-      const cmd = createProjectCommand({ client, log });
-      await cmd.parseAsync(['profiles', 'proj-1'], { from: 'user' });
-      expect(output.join('\n')).toContain('No profiles assigned');
-    });
-  });
-
-  describe('set-profiles', () => {
-    it('sets profiles for a project', async () => {
-      const cmd = createProjectCommand({ client, log });
-      await cmd.parseAsync(['set-profiles', 'proj-1', 'prof-1', 'prof-2'], { from: 'user' });
-      expect(client.put).toHaveBeenCalledWith('/api/v1/projects/proj-1/profiles', {
-        profileIds: ['prof-1', 'prof-2'],
-      });
-      expect(output.join('\n')).toContain('2 profile(s)');
-    });
+  it('creates command with alias', () => {
+    const cmd = createProjectCommand({ client, log });
+    expect(cmd.name()).toBe('project');
+    expect(cmd.alias()).toBe('proj');
   });
 });

src/cli/tests/commands/setup.test.ts

@@ -1,141 +0,0 @@
-import { describe, it, expect, vi, beforeEach } from 'vitest';
-import { createSetupCommand } from '../../src/commands/setup.js';
-import type { ApiClient } from '../../src/api-client.js';
-import type { SetupPromptDeps } from '../../src/commands/setup.js';
-
-function mockClient(): ApiClient {
-  return {
-    get: vi.fn(async () => []),
-    post: vi.fn(async () => ({ id: 'new-id', name: 'test' })),
-    put: vi.fn(async () => ({})),
-    delete: vi.fn(async () => {}),
-  } as unknown as ApiClient;
-}
-
-function mockPrompt(answers: Record<string, string | boolean>): SetupPromptDeps {
-  const answersQueue = { ...answers };
-  return {
-    input: vi.fn(async (message: string) => {
-      for (const [key, val] of Object.entries(answersQueue)) {
-        if (message.toLowerCase().includes(key.toLowerCase()) && typeof val === 'string') {
-          delete answersQueue[key];
-          return val;
-        }
-      }
-      return '';
-    }),
-    password: vi.fn(async () => 'secret-value'),
-    select: vi.fn(async () => 'STDIO') as SetupPromptDeps['select'],
-    confirm: vi.fn(async (message: string) => {
-      if (message.includes('profile')) return true;
-      if (message.includes('secret')) return false;
-      if (message.includes('another')) return false;
-      return false;
-    }),
-  };
-}
-
-describe('setup command', () => {
-  let client: ReturnType<typeof mockClient>;
-  let output: string[];
-  const log = (...args: unknown[]) => output.push(args.map(String).join(' '));
-
-  beforeEach(() => {
-    client = mockClient();
-    output = [];
-  });
-
-  it('creates server with prompted values', async () => {
-    const prompt = mockPrompt({
-      'transport': 'STDIO',
-      'npm package': '@anthropic/slack-mcp',
-      'docker image': '',
-      'description': 'Slack server',
-      'profile name': 'default',
-      'environment variable name': '',
-    });
-
-    const cmd = createSetupCommand({ client, prompt, log });
-    await cmd.parseAsync(['slack'], { from: 'user' });
-
-    expect(client.post).toHaveBeenCalledWith('/api/v1/servers', expect.objectContaining({
-      name: 'slack',
-      transport: 'STDIO',
-    }));
-    expect(output.join('\n')).toContain("Server 'test' created");
-  });
-
-  it('creates profile with env vars', async () => {
-    vi.mocked(client.post)
-      .mockResolvedValueOnce({ id: 'srv-1', name: 'slack' })  // server create
-      .mockResolvedValueOnce({ id: 'prof-1', name: 'default' }); // profile create
-
-    const prompt = mockPrompt({
-      'transport': 'STDIO',
-      'npm package': '',
-      'docker image': '',
-      'description': '',
-      'profile name': 'default',
-    });
-    // Override confirm to create profile and add one env var
-    let confirmCallCount = 0;
-    vi.mocked(prompt.confirm).mockImplementation(async (msg: string) => {
-      confirmCallCount++;
-      if (msg.includes('profile')) return true;
-      if (msg.includes('secret')) return true;
-      if (msg.includes('another')) return false;
-      return false;
-    });
-    // Override input to provide env var name then empty to stop
-    let inputCallCount = 0;
-    vi.mocked(prompt.input).mockImplementation(async (msg: string) => {
-      inputCallCount++;
-      if (msg.includes('Profile name')) return 'default';
-      if (msg.includes('variable name') && inputCallCount <= 8) return 'API_KEY';
-      if (msg.includes('variable name')) return '';
-      return '';
-    });
-
-    const cmd = createSetupCommand({ client, prompt, log });
-    await cmd.parseAsync(['slack'], { from: 'user' });
-
-    expect(client.post).toHaveBeenCalledTimes(2);
-    const profileCall = vi.mocked(client.post).mock.calls[1];
-    expect(profileCall?.[0]).toBe('/api/v1/profiles');
-    expect(profileCall?.[1]).toEqual(expect.objectContaining({
-      name: 'default',
-      serverId: 'srv-1',
-    }));
-  });
-
-  it('exits if server creation fails', async () => {
-    vi.mocked(client.post).mockRejectedValue(new Error('conflict'));
-
-    const prompt = mockPrompt({
-      'npm package': '',
-      'docker image': '',
-      'description': '',
-    });
-
-    const cmd = createSetupCommand({ client, prompt, log });
-    await cmd.parseAsync(['slack'], { from: 'user' });
-
-    expect(output.join('\n')).toContain('Failed to create server');
-    expect(client.post).toHaveBeenCalledTimes(1); // Only server create, no profile
-  });
-
-  it('skips profile creation when declined', async () => {
-    const prompt = mockPrompt({
-      'npm package': '',
-      'docker image': '',
-      'description': '',
-    });
-    vi.mocked(prompt.confirm).mockResolvedValue(false);
-
-    const cmd = createSetupCommand({ client, prompt, log });
-    await cmd.parseAsync(['test-server'], { from: 'user' });
-
-    expect(client.post).toHaveBeenCalledTimes(1); // Only server create
-    expect(output.join('\n')).toContain('Setup complete');
-  });
-});

src/cli/tests/e2e/cli-commands.test.ts

@@ -16,26 +16,21 @@ describe('CLI command registration (e2e)', () => {
     expect(commandNames).toContain('logout');
     expect(commandNames).toContain('get');
     expect(commandNames).toContain('describe');
-    expect(commandNames).toContain('instance');
+    expect(commandNames).toContain('delete');
+    expect(commandNames).toContain('logs');
     expect(commandNames).toContain('apply');
-    expect(commandNames).toContain('setup');
+    expect(commandNames).toContain('create');
+    expect(commandNames).toContain('edit');
     expect(commandNames).toContain('claude');
     expect(commandNames).toContain('project');
+    expect(commandNames).toContain('backup');
+    expect(commandNames).toContain('restore');
   });
 
-  it('instance command has lifecycle subcommands', () => {
+  it('instance command is removed (use get/delete/logs instead)', () => {
     const program = createProgram();
-    const instance = program.commands.find((c) => c.name() === 'instance');
-    expect(instance).toBeDefined();
-
-    const subcommands = instance!.commands.map((c) => c.name());
-    expect(subcommands).toContain('list');
-    expect(subcommands).toContain('start');
-    expect(subcommands).toContain('stop');
-    expect(subcommands).toContain('restart');
-    expect(subcommands).toContain('remove');
-    expect(subcommands).toContain('logs');
-    expect(subcommands).toContain('inspect');
+    const commandNames = program.commands.map((c) => c.name());
+    expect(commandNames).not.toContain('instance');
   });
 
   it('claude command has config management subcommands', () => {
@@ -50,18 +45,11 @@ describe('CLI command registration (e2e)', () => {
     expect(subcommands).toContain('remove');
   });
 
-  it('project command has CRUD subcommands', () => {
+  it('project command exists with alias', () => {
     const program = createProgram();
     const project = program.commands.find((c) => c.name() === 'project');
     expect(project).toBeDefined();
-
-    const subcommands = project!.commands.map((c) => c.name());
-    expect(subcommands).toContain('list');
-    expect(subcommands).toContain('create');
-    expect(subcommands).toContain('delete');
-    expect(subcommands).toContain('show');
-    expect(subcommands).toContain('profiles');
-    expect(subcommands).toContain('set-profiles');
+    expect(project!.alias()).toBe('proj');
   });
 
   it('displays version', () => {

src/db/prisma/migrations/20260222121228_add_external_url_command_port/migration.sql

@@ -0,0 +1,204 @@
+-- CreateEnum
+CREATE TYPE "Role" AS ENUM ('USER', 'ADMIN');
+
+-- CreateEnum
+CREATE TYPE "Transport" AS ENUM ('STDIO', 'SSE', 'STREAMABLE_HTTP');
+
+-- CreateEnum
+CREATE TYPE "InstanceStatus" AS ENUM ('STARTING', 'RUNNING', 'STOPPING', 'STOPPED', 'ERROR');
+
+-- CreateTable
+CREATE TABLE "User" (
+    "id" TEXT NOT NULL,
+    "email" TEXT NOT NULL,
+    "name" TEXT,
+    "passwordHash" TEXT NOT NULL,
+    "role" "Role" NOT NULL DEFAULT 'USER',
+    "version" INTEGER NOT NULL DEFAULT 1,
+    "createdAt" TIMESTAMP(3) NOT NULL DEFAULT CURRENT_TIMESTAMP,
+    "updatedAt" TIMESTAMP(3) NOT NULL,
+
+    CONSTRAINT "User_pkey" PRIMARY KEY ("id")
+);
+
+-- CreateTable
+CREATE TABLE "Session" (
+    "id" TEXT NOT NULL,
+    "token" TEXT NOT NULL,
+    "userId" TEXT NOT NULL,
+    "expiresAt" TIMESTAMP(3) NOT NULL,
+    "createdAt" TIMESTAMP(3) NOT NULL DEFAULT CURRENT_TIMESTAMP,
+
+    CONSTRAINT "Session_pkey" PRIMARY KEY ("id")
+);
+
+-- CreateTable
+CREATE TABLE "McpServer" (
+    "id" TEXT NOT NULL,
+    "name" TEXT NOT NULL,
+    "description" TEXT NOT NULL DEFAULT '',
+    "packageName" TEXT,
+    "dockerImage" TEXT,
+    "transport" "Transport" NOT NULL DEFAULT 'STDIO',
+    "repositoryUrl" TEXT,
+    "externalUrl" TEXT,
+    "command" JSONB,
+    "containerPort" INTEGER,
+    "envTemplate" JSONB NOT NULL DEFAULT '[]',
+    "version" INTEGER NOT NULL DEFAULT 1,
+    "createdAt" TIMESTAMP(3) NOT NULL DEFAULT CURRENT_TIMESTAMP,
+    "updatedAt" TIMESTAMP(3) NOT NULL,
+
+    CONSTRAINT "McpServer_pkey" PRIMARY KEY ("id")
+);
+
+-- CreateTable
+CREATE TABLE "McpProfile" (
+    "id" TEXT NOT NULL,
+    "name" TEXT NOT NULL,
+    "serverId" TEXT NOT NULL,
+    "permissions" JSONB NOT NULL DEFAULT '[]',
+    "envOverrides" JSONB NOT NULL DEFAULT '{}',
+    "version" INTEGER NOT NULL DEFAULT 1,
+    "createdAt" TIMESTAMP(3) NOT NULL DEFAULT CURRENT_TIMESTAMP,
+    "updatedAt" TIMESTAMP(3) NOT NULL,
+
+    CONSTRAINT "McpProfile_pkey" PRIMARY KEY ("id")
+);
+
+-- CreateTable
+CREATE TABLE "Project" (
+    "id" TEXT NOT NULL,
+    "name" TEXT NOT NULL,
+    "description" TEXT NOT NULL DEFAULT '',
+    "ownerId" TEXT NOT NULL,
+    "version" INTEGER NOT NULL DEFAULT 1,
+    "createdAt" TIMESTAMP(3) NOT NULL DEFAULT CURRENT_TIMESTAMP,
+    "updatedAt" TIMESTAMP(3) NOT NULL,
+
+    CONSTRAINT "Project_pkey" PRIMARY KEY ("id")
+);
+
+-- CreateTable
+CREATE TABLE "ProjectMcpProfile" (
+    "id" TEXT NOT NULL,
+    "projectId" TEXT NOT NULL,
+    "profileId" TEXT NOT NULL,
+
+    CONSTRAINT "ProjectMcpProfile_pkey" PRIMARY KEY ("id")
+);
+
+-- CreateTable
+CREATE TABLE "McpInstance" (
+    "id" TEXT NOT NULL,
+    "serverId" TEXT NOT NULL,
+    "containerId" TEXT,
+    "status" "InstanceStatus" NOT NULL DEFAULT 'STOPPED',
+    "port" INTEGER,
+    "metadata" JSONB NOT NULL DEFAULT '{}',
+    "version" INTEGER NOT NULL DEFAULT 1,
+    "createdAt" TIMESTAMP(3) NOT NULL DEFAULT CURRENT_TIMESTAMP,
+    "updatedAt" TIMESTAMP(3) NOT NULL,
+
+    CONSTRAINT "McpInstance_pkey" PRIMARY KEY ("id")
+);
+
+-- CreateTable
+CREATE TABLE "AuditLog" (
+    "id" TEXT NOT NULL,
+    "userId" TEXT NOT NULL,
+    "action" TEXT NOT NULL,
+    "resource" TEXT NOT NULL,
+    "resourceId" TEXT,
+    "details" JSONB NOT NULL DEFAULT '{}',
+    "createdAt" TIMESTAMP(3) NOT NULL DEFAULT CURRENT_TIMESTAMP,
+
+    CONSTRAINT "AuditLog_pkey" PRIMARY KEY ("id")
+);
+
+-- CreateIndex
+CREATE UNIQUE INDEX "User_email_key" ON "User"("email");
+
+-- CreateIndex
+CREATE INDEX "User_email_idx" ON "User"("email");
+
+-- CreateIndex
+CREATE UNIQUE INDEX "Session_token_key" ON "Session"("token");
+
+-- CreateIndex
+CREATE INDEX "Session_token_idx" ON "Session"("token");
+
+-- CreateIndex
+CREATE INDEX "Session_userId_idx" ON "Session"("userId");
+
+-- CreateIndex
+CREATE INDEX "Session_expiresAt_idx" ON "Session"("expiresAt");
+
+-- CreateIndex
+CREATE UNIQUE INDEX "McpServer_name_key" ON "McpServer"("name");
+
+-- CreateIndex
+CREATE INDEX "McpServer_name_idx" ON "McpServer"("name");
+
+-- CreateIndex
+CREATE INDEX "McpProfile_serverId_idx" ON "McpProfile"("serverId");
+
+-- CreateIndex
+CREATE UNIQUE INDEX "McpProfile_name_serverId_key" ON "McpProfile"("name", "serverId");
+
+-- CreateIndex
+CREATE UNIQUE INDEX "Project_name_key" ON "Project"("name");
+
+-- CreateIndex
+CREATE INDEX "Project_name_idx" ON "Project"("name");
+
+-- CreateIndex
+CREATE INDEX "Project_ownerId_idx" ON "Project"("ownerId");
+
+-- CreateIndex
+CREATE INDEX "ProjectMcpProfile_projectId_idx" ON "ProjectMcpProfile"("projectId");
+
+-- CreateIndex
+CREATE INDEX "ProjectMcpProfile_profileId_idx" ON "ProjectMcpProfile"("profileId");
+
+-- CreateIndex
+CREATE UNIQUE INDEX "ProjectMcpProfile_projectId_profileId_key" ON "ProjectMcpProfile"("projectId", "profileId");
+
+-- CreateIndex
+CREATE INDEX "McpInstance_serverId_idx" ON "McpInstance"("serverId");
+
+-- CreateIndex
+CREATE INDEX "McpInstance_status_idx" ON "McpInstance"("status");
+
+-- CreateIndex
+CREATE INDEX "AuditLog_userId_idx" ON "AuditLog"("userId");
+
+-- CreateIndex
+CREATE INDEX "AuditLog_action_idx" ON "AuditLog"("action");
+
+-- CreateIndex
+CREATE INDEX "AuditLog_resource_idx" ON "AuditLog"("resource");
+
+-- CreateIndex
+CREATE INDEX "AuditLog_createdAt_idx" ON "AuditLog"("createdAt");
+
+-- AddForeignKey
+ALTER TABLE "Session" ADD CONSTRAINT "Session_userId_fkey" FOREIGN KEY ("userId") REFERENCES "User"("id") ON DELETE CASCADE ON UPDATE CASCADE;
+
+-- AddForeignKey
+ALTER TABLE "McpProfile" ADD CONSTRAINT "McpProfile_serverId_fkey" FOREIGN KEY ("serverId") REFERENCES "McpServer"("id") ON DELETE CASCADE ON UPDATE CASCADE;
+
+-- AddForeignKey
+ALTER TABLE "Project" ADD CONSTRAINT "Project_ownerId_fkey" FOREIGN KEY ("ownerId") REFERENCES "User"("id") ON DELETE CASCADE ON UPDATE CASCADE;
+
+-- AddForeignKey
+ALTER TABLE "ProjectMcpProfile" ADD CONSTRAINT "ProjectMcpProfile_projectId_fkey" FOREIGN KEY ("projectId") REFERENCES "Project"("id") ON DELETE CASCADE ON UPDATE CASCADE;
+
+-- AddForeignKey
+ALTER TABLE "ProjectMcpProfile" ADD CONSTRAINT "ProjectMcpProfile_profileId_fkey" FOREIGN KEY ("profileId") REFERENCES "McpProfile"("id") ON DELETE CASCADE ON UPDATE CASCADE;
+
+-- AddForeignKey
+ALTER TABLE "McpInstance" ADD CONSTRAINT "McpInstance_serverId_fkey" FOREIGN KEY ("serverId") REFERENCES "McpServer"("id") ON DELETE CASCADE ON UPDATE CASCADE;
+
+-- AddForeignKey
+ALTER TABLE "AuditLog" ADD CONSTRAINT "AuditLog_userId_fkey" FOREIGN KEY ("userId") REFERENCES "User"("id") ON DELETE CASCADE ON UPDATE CASCADE;

src/db/prisma/migrations/migration_lock.toml

@@ -0,0 +1,3 @@
+# Please do not edit this file manually
+# It should be added in your version-control system (e.g., Git)
+provider = "postgresql"

src/db/prisma/schema.prisma

@@ -57,12 +57,15 @@ model McpServer {
   dockerImage   String?
   transport     Transport       @default(STDIO)
   repositoryUrl String?
-  envTemplate   Json            @default("[]")
+  externalUrl   String?
+  command       Json?
+  containerPort Int?
+  replicas      Int             @default(1)
+  env           Json            @default("[]")
   version       Int             @default(1)
   createdAt     DateTime        @default(now())
   updatedAt     DateTime        @updatedAt
 
-  profiles  McpProfile[]
   instances McpInstance[]
 
   @@index([name])
@@ -74,23 +77,17 @@ enum Transport {
   STREAMABLE_HTTP
 }
 
-// ── MCP Profiles ──
+// ── Secrets ──
 
-model McpProfile {
-  id          String   @id @default(cuid())
-  name        String
-  serverId    String
-  permissions Json     @default("[]")
-  envOverrides Json    @default("{}")
-  version     Int      @default(1)
-  createdAt   DateTime @default(now())
-  updatedAt   DateTime @updatedAt
+model Secret {
+  id        String   @id @default(cuid())
+  name      String   @unique
+  data      Json     @default("{}")
+  version   Int      @default(1)
+  createdAt DateTime @default(now())
+  updatedAt DateTime @updatedAt
 
-  server   McpServer            @relation(fields: [serverId], references: [id], onDelete: Cascade)
-  projects ProjectMcpProfile[]
-
-  @@unique([name, serverId])
-  @@index([serverId])
+  @@index([name])
 }
 
 // ── Projects ──
@@ -105,27 +102,11 @@ model Project {
   updatedAt   DateTime @updatedAt
 
   owner    User                 @relation(fields: [ownerId], references: [id], onDelete: Cascade)
-  profiles ProjectMcpProfile[]
 
   @@index([name])
   @@index([ownerId])
 }
 
-// ── Project <-> Profile join table ──
-
-model ProjectMcpProfile {
-  id        String @id @default(cuid())
-  projectId String
-  profileId String
-
-  project Project    @relation(fields: [projectId], references: [id], onDelete: Cascade)
-  profile McpProfile @relation(fields: [profileId], references: [id], onDelete: Cascade)
-
-  @@unique([projectId, profileId])
-  @@index([projectId])
-  @@index([profileId])
-}
-
 // ── MCP Instances (running containers) ──
 
 model McpInstance {

src/db/src/index.ts

@@ -4,9 +4,8 @@ export type {
   User,
   Session,
   McpServer,
-  McpProfile,
+  Secret,
   Project,
-  ProjectMcpProfile,
   McpInstance,
   AuditLog,
   Role,

src/db/src/seed/index.ts

@@ -6,11 +6,10 @@ export interface SeedServer {
   packageName: string;
   transport: 'STDIO' | 'SSE' | 'STREAMABLE_HTTP';
   repositoryUrl: string;
-  envTemplate: Array<{
+  env: Array<{
     name: string;
-    description: string;
-    isSecret: boolean;
-    setupUrl?: string;
+    value?: string;
+    valueFrom?: { secretRef: { name: string; key: string } };
   }>;
 }
 
@@ -21,19 +20,7 @@ export const defaultServers: SeedServer[] = [
     packageName: '@anthropic/slack-mcp',
     transport: 'STDIO',
     repositoryUrl: 'https://github.com/modelcontextprotocol/servers/tree/main/src/slack',
-    envTemplate: [
-      {
-        name: 'SLACK_BOT_TOKEN',
-        description: 'Slack Bot User OAuth Token (xoxb-...)',
-        isSecret: true,
-        setupUrl: 'https://api.slack.com/apps',
-      },
-      {
-        name: 'SLACK_TEAM_ID',
-        description: 'Slack Workspace Team ID',
-        isSecret: false,
-      },
-    ],
+    env: [],
   },
   {
     name: 'jira',
@@ -41,24 +28,7 @@ export const defaultServers: SeedServer[] = [
     packageName: '@anthropic/jira-mcp',
     transport: 'STDIO',
     repositoryUrl: 'https://github.com/modelcontextprotocol/servers/tree/main/src/jira',
-    envTemplate: [
-      {
-        name: 'JIRA_URL',
-        description: 'Jira instance URL (e.g., https://company.atlassian.net)',
-        isSecret: false,
-      },
-      {
-        name: 'JIRA_EMAIL',
-        description: 'Jira account email',
-        isSecret: false,
-      },
-      {
-        name: 'JIRA_API_TOKEN',
-        description: 'Jira API token',
-        isSecret: true,
-        setupUrl: 'https://id.atlassian.com/manage-profile/security/api-tokens',
-      },
-    ],
+    env: [],
   },
   {
     name: 'github',
@@ -66,14 +36,7 @@ export const defaultServers: SeedServer[] = [
     packageName: '@anthropic/github-mcp',
     transport: 'STDIO',
     repositoryUrl: 'https://github.com/modelcontextprotocol/servers/tree/main/src/github',
-    envTemplate: [
-      {
-        name: 'GITHUB_TOKEN',
-        description: 'GitHub Personal Access Token',
-        isSecret: true,
-        setupUrl: 'https://github.com/settings/tokens',
-      },
-    ],
+    env: [],
   },
   {
     name: 'terraform',
@@ -81,7 +44,7 @@ export const defaultServers: SeedServer[] = [
     packageName: '@anthropic/terraform-mcp',
     transport: 'STDIO',
     repositoryUrl: 'https://github.com/modelcontextprotocol/servers/tree/main/src/terraform',
-    envTemplate: [],
+    env: [],
   },
 ];
 
@@ -99,7 +62,7 @@ export async function seedMcpServers(
         packageName: server.packageName,
         transport: server.transport,
         repositoryUrl: server.repositoryUrl,
-        envTemplate: server.envTemplate,
+        env: server.env,
       },
       create: {
         name: server.name,
@@ -107,7 +70,7 @@ export async function seedMcpServers(
         packageName: server.packageName,
         transport: server.transport,
         repositoryUrl: server.repositoryUrl,
-        envTemplate: server.envTemplate,
+        env: server.env,
       },
     });
     created++;

src/db/tests/helpers.ts

@@ -48,9 +48,8 @@ export async function cleanupTestDb(): Promise<void> {
 export async function clearAllTables(client: PrismaClient): Promise<void> {
   // Delete in order respecting foreign keys
   await client.auditLog.deleteMany();
-  await client.projectMcpProfile.deleteMany();
   await client.mcpInstance.deleteMany();
-  await client.mcpProfile.deleteMany();
+  await client.secret.deleteMany();
   await client.session.deleteMany();
   await client.project.deleteMany();
   await client.mcpServer.deleteMany();

src/db/tests/models.test.ts

@@ -123,7 +123,7 @@ describe('McpServer', () => {
     const server = await createServer();
     expect(server.transport).toBe('STDIO');
     expect(server.version).toBe(1);
-    expect(server.envTemplate).toEqual([]);
+    expect(server.env).toEqual([]);
   });
 
   it('enforces unique name', async () => {
@@ -131,18 +131,18 @@ describe('McpServer', () => {
     await expect(createServer({ name: 'slack' })).rejects.toThrow();
   });
 
-  it('stores envTemplate as JSON', async () => {
+  it('stores env as JSON', async () => {
     const server = await prisma.mcpServer.create({
       data: {
         name: 'with-env',
-        envTemplate: [
-          { name: 'API_KEY', description: 'Key', isSecret: true },
+        env: [
+          { name: 'API_KEY', value: 'test-key' },
         ],
       },
     });
-    const envTemplate = server.envTemplate as Array<{ name: string }>;
-    expect(envTemplate).toHaveLength(1);
-    expect(envTemplate[0].name).toBe('API_KEY');
+    const env = server.env as Array<{ name: string }>;
+    expect(env).toHaveLength(1);
+    expect(env[0].name).toBe('API_KEY');
   });
 
   it('supports SSE transport', async () => {
@@ -151,43 +151,46 @@ describe('McpServer', () => {
   });
 });
 
-// ── McpProfile model ──
+// ── Secret model ──
 
-describe('McpProfile', () => {
-  it('creates a profile linked to server', async () => {
-    const server = await createServer();
-    const profile = await prisma.mcpProfile.create({
+describe('Secret', () => {
+  it('creates a secret with defaults', async () => {
+    const secret = await prisma.secret.create({
+      data: { name: 'my-secret' },
+    });
+    expect(secret.name).toBe('my-secret');
+    expect(secret.data).toEqual({});
+    expect(secret.version).toBe(1);
+  });
+
+  it('stores key-value data as JSON', async () => {
+    const secret = await prisma.secret.create({
       data: {
-        name: 'readonly',
-        serverId: server.id,
-        permissions: ['read'],
+        name: 'api-keys',
+        data: { API_KEY: 'test-key', API_SECRET: 'test-secret' },
       },
     });
-    expect(profile.name).toBe('readonly');
-    expect(profile.serverId).toBe(server.id);
+    const data = secret.data as Record<string, string>;
+    expect(data['API_KEY']).toBe('test-key');
+    expect(data['API_SECRET']).toBe('test-secret');
   });
 
-  it('enforces unique name per server', async () => {
-    const server = await createServer();
-    const data = { name: 'default', serverId: server.id };
-    await prisma.mcpProfile.create({ data });
-    await expect(prisma.mcpProfile.create({ data })).rejects.toThrow();
+  it('enforces unique name', async () => {
+    await prisma.secret.create({ data: { name: 'dup-secret' } });
+    await expect(prisma.secret.create({ data: { name: 'dup-secret' } })).rejects.toThrow();
   });
 
-  it('allows same profile name on different servers', async () => {
-    const server1 = await createServer({ name: 'server-1' });
-    const server2 = await createServer({ name: 'server-2' });
-    await prisma.mcpProfile.create({ data: { name: 'default', serverId: server1.id } });
-    const profile2 = await prisma.mcpProfile.create({ data: { name: 'default', serverId: server2.id } });
-    expect(profile2.name).toBe('default');
-  });
-
-  it('cascades delete when server is deleted', async () => {
-    const server = await createServer();
-    await prisma.mcpProfile.create({ data: { name: 'test', serverId: server.id } });
-    await prisma.mcpServer.delete({ where: { id: server.id } });
-    const profiles = await prisma.mcpProfile.findMany({ where: { serverId: server.id } });
-    expect(profiles).toHaveLength(0);
+  it('updates data', async () => {
+    const secret = await prisma.secret.create({
+      data: { name: 'updatable', data: { KEY: 'old' } },
+    });
+    const updated = await prisma.secret.update({
+      where: { id: secret.id },
+      data: { data: { KEY: 'new', EXTRA: 'added' } },
+    });
+    const data = updated.data as Record<string, string>;
+    expect(data['KEY']).toBe('new');
+    expect(data['EXTRA']).toBe('added');
   });
 });
 
@@ -220,62 +223,6 @@ describe('Project', () => {
   });
 });
 
-// ── ProjectMcpProfile (join table) ──
-
-describe('ProjectMcpProfile', () => {
-  it('links project to profile', async () => {
-    const user = await createUser();
-    const server = await createServer();
-    const profile = await prisma.mcpProfile.create({
-      data: { name: 'default', serverId: server.id },
-    });
-    const project = await prisma.project.create({
-      data: { name: 'test-project', ownerId: user.id },
-    });
-
-    const link = await prisma.projectMcpProfile.create({
-      data: { projectId: project.id, profileId: profile.id },
-    });
-    expect(link.projectId).toBe(project.id);
-    expect(link.profileId).toBe(profile.id);
-  });
-
-  it('enforces unique project+profile combination', async () => {
-    const user = await createUser();
-    const server = await createServer();
-    const profile = await prisma.mcpProfile.create({
-      data: { name: 'default', serverId: server.id },
-    });
-    const project = await prisma.project.create({
-      data: { name: 'test-project', ownerId: user.id },
-    });
-
-    const data = { projectId: project.id, profileId: profile.id };
-    await prisma.projectMcpProfile.create({ data });
-    await expect(prisma.projectMcpProfile.create({ data })).rejects.toThrow();
-  });
-
-  it('loads profiles through project include', async () => {
-    const user = await createUser();
-    const server = await createServer();
-    const profile = await prisma.mcpProfile.create({
-      data: { name: 'slack-ro', serverId: server.id },
-    });
-    const project = await prisma.project.create({
-      data: { name: 'reports', ownerId: user.id },
-    });
-    await prisma.projectMcpProfile.create({
-      data: { projectId: project.id, profileId: profile.id },
-    });
-
-    const loaded = await prisma.project.findUnique({
-      where: { id: project.id },
-      include: { profiles: { include: { profile: true } } },
-    });
-    expect(loaded!.profiles).toHaveLength(1);
-    expect(loaded!.profiles[0].profile.name).toBe('slack-ro');
-  });
-});
 
 // ── McpInstance model ──
 

src/db/tests/seed.test.ts

@@ -41,13 +41,11 @@ describe('seedMcpServers', () => {
     expect(servers).toHaveLength(defaultServers.length);
   });
 
-  it('seeds envTemplate correctly', async () => {
+  it('seeds env correctly', async () => {
     await seedMcpServers(prisma);
     const slack = await prisma.mcpServer.findUnique({ where: { name: 'slack' } });
-    const envTemplate = slack!.envTemplate as Array<{ name: string; isSecret: boolean }>;
-    expect(envTemplate).toHaveLength(2);
-    expect(envTemplate[0].name).toBe('SLACK_BOT_TOKEN');
-    expect(envTemplate[0].isSecret).toBe(true);
+    const env = slack!.env as Array<{ name: string; value?: string }>;
+    expect(env).toEqual([]);
   });
 
   it('accepts custom server list', async () => {
@@ -58,7 +56,7 @@ describe('seedMcpServers', () => {
         packageName: '@test/custom',
         transport: 'STDIO' as const,
         repositoryUrl: 'https://example.com',
-        envTemplate: [],
+        env: [],
       },
     ];
     const count = await seedMcpServers(prisma, custom);

src/mcpd/src/main.ts

@@ -5,14 +5,14 @@ import { createServer } from './server.js';
 import { setupGracefulShutdown } from './utils/index.js';
 import {
   McpServerRepository,
-  McpProfileRepository,
+  SecretRepository,
   McpInstanceRepository,
   ProjectRepository,
   AuditLogRepository,
 } from './repositories/index.js';
 import {
   McpServerService,
-  McpProfileService,
+  SecretService,
   InstanceService,
   ProjectService,
   AuditLogService,
@@ -26,7 +26,7 @@ import {
 } from './services/index.js';
 import {
   registerMcpServerRoutes,
-  registerMcpProfileRoutes,
+  registerSecretRoutes,
   registerInstanceRoutes,
   registerProjectRoutes,
   registerAuditLogRoutes,
@@ -50,7 +50,7 @@ async function main(): Promise<void> {
 
   // Repositories
   const serverRepo = new McpServerRepository(prisma);
-  const profileRepo = new McpProfileRepository(prisma);
+  const secretRepo = new SecretRepository(prisma);
   const instanceRepo = new McpInstanceRepository(prisma);
   const projectRepo = new ProjectRepository(prisma);
   const auditLogRepo = new AuditLogRepository(prisma);
@@ -60,16 +60,17 @@ async function main(): Promise<void> {
 
   // Services
   const serverService = new McpServerService(serverRepo);
-  const profileService = new McpProfileService(profileRepo, serverRepo);
-  const instanceService = new InstanceService(instanceRepo, serverRepo, orchestrator);
-  const projectService = new ProjectService(projectRepo, profileRepo, serverRepo);
+  const instanceService = new InstanceService(instanceRepo, serverRepo, orchestrator, secretRepo);
+  serverService.setInstanceService(instanceService);
+  const secretService = new SecretService(secretRepo);
+  const projectService = new ProjectService(projectRepo, serverRepo);
   const auditLogService = new AuditLogService(auditLogRepo);
   const metricsCollector = new MetricsCollector();
   const healthAggregator = new HealthAggregator(metricsCollector, orchestrator);
-  const backupService = new BackupService(serverRepo, profileRepo, projectRepo);
-  const restoreService = new RestoreService(serverRepo, profileRepo, projectRepo);
+  const backupService = new BackupService(serverRepo, projectRepo, secretRepo);
+  const restoreService = new RestoreService(serverRepo, projectRepo, secretRepo);
   const authService = new AuthService(prisma);
-  const mcpProxyService = new McpProxyService(instanceRepo);
+  const mcpProxyService = new McpProxyService(instanceRepo, serverRepo);
 
   // Server
   const app = await createServer(config, {
@@ -86,8 +87,8 @@ async function main(): Promise<void> {
   });
 
   // Routes
-  registerMcpServerRoutes(app, serverService);
-  registerMcpProfileRoutes(app, profileService);
+  registerMcpServerRoutes(app, serverService, instanceService);
+  registerSecretRoutes(app, secretService);
   registerInstanceRoutes(app, instanceService);
   registerProjectRoutes(app, projectService);
   registerAuditLogRoutes(app, auditLogService);

src/mcpd/src/repositories/index.ts

@@ -1,6 +1,6 @@
-export type { IMcpServerRepository, IMcpProfileRepository, IMcpInstanceRepository, IAuditLogRepository, AuditLogFilter } from './interfaces.js';
+export type { IMcpServerRepository, IMcpInstanceRepository, ISecretRepository, IAuditLogRepository, AuditLogFilter } from './interfaces.js';
 export { McpServerRepository } from './mcp-server.repository.js';
-export { McpProfileRepository } from './mcp-profile.repository.js';
+export { SecretRepository } from './secret.repository.js';
 export type { IProjectRepository } from './project.repository.js';
 export { ProjectRepository } from './project.repository.js';
 export { McpInstanceRepository } from './mcp-instance.repository.js';

src/mcpd/src/repositories/interfaces.ts

@@ -1,6 +1,6 @@
-import type { McpServer, McpProfile, McpInstance, AuditLog, InstanceStatus } from '@prisma/client';
+import type { McpServer, McpInstance, AuditLog, Secret, InstanceStatus } from '@prisma/client';
 import type { CreateMcpServerInput, UpdateMcpServerInput } from '../validation/mcp-server.schema.js';
-import type { CreateMcpProfileInput, UpdateMcpProfileInput } from '../validation/mcp-profile.schema.js';
+import type { CreateSecretInput, UpdateSecretInput } from '../validation/secret.schema.js';
 
 export interface IMcpServerRepository {
   findAll(): Promise<McpServer[]>;
@@ -20,12 +20,12 @@ export interface IMcpInstanceRepository {
   delete(id: string): Promise<void>;
 }
 
-export interface IMcpProfileRepository {
-  findAll(serverId?: string): Promise<McpProfile[]>;
-  findById(id: string): Promise<McpProfile | null>;
-  findByServerAndName(serverId: string, name: string): Promise<McpProfile | null>;
-  create(data: CreateMcpProfileInput): Promise<McpProfile>;
-  update(id: string, data: UpdateMcpProfileInput): Promise<McpProfile>;
+export interface ISecretRepository {
+  findAll(): Promise<Secret[]>;
+  findById(id: string): Promise<Secret | null>;
+  findByName(name: string): Promise<Secret | null>;
+  create(data: CreateSecretInput): Promise<Secret>;
+  update(id: string, data: UpdateSecretInput): Promise<Secret>;
   delete(id: string): Promise<void>;
 }
 

src/mcpd/src/repositories/mcp-profile.repository.ts

@@ -1,46 +0,0 @@
-import type { PrismaClient, McpProfile } from '@prisma/client';
-import type { IMcpProfileRepository } from './interfaces.js';
-import type { CreateMcpProfileInput, UpdateMcpProfileInput } from '../validation/mcp-profile.schema.js';
-
-export class McpProfileRepository implements IMcpProfileRepository {
-  constructor(private readonly prisma: PrismaClient) {}
-
-  async findAll(serverId?: string): Promise<McpProfile[]> {
-    const where = serverId !== undefined ? { serverId } : {};
-    return this.prisma.mcpProfile.findMany({ where, orderBy: { name: 'asc' } });
-  }
-
-  async findById(id: string): Promise<McpProfile | null> {
-    return this.prisma.mcpProfile.findUnique({ where: { id } });
-  }
-
-  async findByServerAndName(serverId: string, name: string): Promise<McpProfile | null> {
-    return this.prisma.mcpProfile.findUnique({
-      where: { name_serverId: { name, serverId } },
-    });
-  }
-
-  async create(data: CreateMcpProfileInput): Promise<McpProfile> {
-    return this.prisma.mcpProfile.create({
-      data: {
-        name: data.name,
-        serverId: data.serverId,
-        permissions: data.permissions,
-        envOverrides: data.envOverrides,
-      },
-    });
-  }
-
-  async update(id: string, data: UpdateMcpProfileInput): Promise<McpProfile> {
-    const updateData: Record<string, unknown> = {};
-    if (data.name !== undefined) updateData['name'] = data.name;
-    if (data.permissions !== undefined) updateData['permissions'] = data.permissions;
-    if (data.envOverrides !== undefined) updateData['envOverrides'] = data.envOverrides;
-
-    return this.prisma.mcpProfile.update({ where: { id }, data: updateData });
-  }
-
-  async delete(id: string): Promise<void> {
-    await this.prisma.mcpProfile.delete({ where: { id } });
-  }
-}

src/mcpd/src/repositories/mcp-server.repository.ts

@@ -1,4 +1,4 @@
-import type { PrismaClient, McpServer } from '@prisma/client';
+import { type PrismaClient, type McpServer, Prisma } from '@prisma/client';
 import type { IMcpServerRepository } from './interfaces.js';
 import type { CreateMcpServerInput, UpdateMcpServerInput } from '../validation/mcp-server.schema.js';
 
@@ -26,7 +26,11 @@ export class McpServerRepository implements IMcpServerRepository {
         dockerImage: data.dockerImage ?? null,
         transport: data.transport,
         repositoryUrl: data.repositoryUrl ?? null,
-        envTemplate: data.envTemplate,
+        externalUrl: data.externalUrl ?? null,
+        command: data.command ?? Prisma.DbNull,
+        containerPort: data.containerPort ?? null,
+        replicas: data.replicas,
+        env: data.env,
       },
     });
   }
@@ -38,7 +42,11 @@ export class McpServerRepository implements IMcpServerRepository {
     if (data.dockerImage !== undefined) updateData['dockerImage'] = data.dockerImage;
     if (data.transport !== undefined) updateData['transport'] = data.transport;
     if (data.repositoryUrl !== undefined) updateData['repositoryUrl'] = data.repositoryUrl;
-    if (data.envTemplate !== undefined) updateData['envTemplate'] = data.envTemplate;
+    if (data.externalUrl !== undefined) updateData['externalUrl'] = data.externalUrl;
+    if (data.command !== undefined) updateData['command'] = data.command;
+    if (data.containerPort !== undefined) updateData['containerPort'] = data.containerPort;
+    if (data.replicas !== undefined) updateData['replicas'] = data.replicas;
+    if (data.env !== undefined) updateData['env'] = data.env;
 
     return this.prisma.mcpServer.update({ where: { id }, data: updateData });
   }

src/mcpd/src/repositories/project.repository.ts

@@ -8,8 +8,6 @@ export interface IProjectRepository {
   create(data: CreateProjectInput & { ownerId: string }): Promise<Project>;
   update(id: string, data: UpdateProjectInput): Promise<Project>;
   delete(id: string): Promise<void>;
-  setProfiles(projectId: string, profileIds: string[]): Promise<void>;
-  getProfileIds(projectId: string): Promise<string[]>;
 }
 
 export class ProjectRepository implements IProjectRepository {
@@ -48,22 +46,4 @@ export class ProjectRepository implements IProjectRepository {
     await this.prisma.project.delete({ where: { id } });
   }
 
-  async setProfiles(projectId: string, profileIds: string[]): Promise<void> {
-    await this.prisma.$transaction([
-      this.prisma.projectMcpProfile.deleteMany({ where: { projectId } }),
-      ...profileIds.map((profileId) =>
-        this.prisma.projectMcpProfile.create({
-          data: { projectId, profileId },
-        }),
-      ),
-    ]);
-  }
-
-  async getProfileIds(projectId: string): Promise<string[]> {
-    const links = await this.prisma.projectMcpProfile.findMany({
-      where: { projectId },
-      select: { profileId: true },
-    });
-    return links.map((l) => l.profileId);
-  }
 }

src/mcpd/src/repositories/secret.repository.ts

@@ -0,0 +1,39 @@
+import { type PrismaClient, type Secret } from '@prisma/client';
+import type { ISecretRepository } from './interfaces.js';
+import type { CreateSecretInput, UpdateSecretInput } from '../validation/secret.schema.js';
+
+export class SecretRepository implements ISecretRepository {
+  constructor(private readonly prisma: PrismaClient) {}
+
+  async findAll(): Promise<Secret[]> {
+    return this.prisma.secret.findMany({ orderBy: { name: 'asc' } });
+  }
+
+  async findById(id: string): Promise<Secret | null> {
+    return this.prisma.secret.findUnique({ where: { id } });
+  }
+
+  async findByName(name: string): Promise<Secret | null> {
+    return this.prisma.secret.findUnique({ where: { name } });
+  }
+
+  async create(data: CreateSecretInput): Promise<Secret> {
+    return this.prisma.secret.create({
+      data: {
+        name: data.name,
+        data: data.data,
+      },
+    });
+  }
+
+  async update(id: string, data: UpdateSecretInput): Promise<Secret> {
+    return this.prisma.secret.update({
+      where: { id },
+      data: { data: data.data },
+    });
+  }
+
+  async delete(id: string): Promise<void> {
+    await this.prisma.secret.delete({ where: { id } });
+  }
+}

src/mcpd/src/routes/backup.ts

@@ -13,7 +13,7 @@ export function registerBackupRoutes(app: FastifyInstance, deps: BackupDeps): vo
   app.post<{
     Body: {
       password?: string;
-      resources?: Array<'servers' | 'profiles' | 'projects'>;
+      resources?: Array<'servers' | 'secrets' | 'projects'>;
     };
   }>('/api/v1/backup', async (request) => {
     const opts: BackupOptions = {};
@@ -51,7 +51,7 @@ export function registerBackupRoutes(app: FastifyInstance, deps: BackupDeps): vo
 
     const result = await deps.restoreService.restore(bundle, restoreOpts);
 
-    if (result.errors.length > 0 && result.serversCreated === 0 && result.profilesCreated === 0 && result.projectsCreated === 0) {
+    if (result.errors.length > 0 && result.serversCreated === 0 && result.secretsCreated === 0 && result.projectsCreated === 0) {
       reply.code(422);
     }
 

src/mcpd/src/routes/index.ts

@@ -1,7 +1,7 @@
 export { registerHealthRoutes } from './health.js';
 export type { HealthDeps } from './health.js';
 export { registerMcpServerRoutes } from './mcp-servers.js';
-export { registerMcpProfileRoutes } from './mcp-profiles.js';
+export { registerSecretRoutes } from './secrets.js';
 export { registerProjectRoutes } from './projects.js';
 export { registerInstanceRoutes } from './instances.js';
 export { registerAuditLogRoutes } from './audit-logs.js';

src/mcpd/src/routes/instances.ts

@@ -10,40 +10,17 @@ export function registerInstanceRoutes(app: FastifyInstance, service: InstanceSe
     return service.getById(request.params.id);
   });
 
-  app.post<{ Body: { serverId: string; env?: Record<string, string>; hostPort?: number } }>(
-    '/api/v1/instances',
-    async (request, reply) => {
-      const { serverId } = request.body;
-      const opts: { env?: Record<string, string>; hostPort?: number } = {};
-      if (request.body.env) {
-        opts.env = request.body.env;
-      }
-      if (request.body.hostPort !== undefined) {
-        opts.hostPort = request.body.hostPort;
-      }
-      const instance = await service.start(serverId, opts);
-      reply.code(201);
-      return instance;
-    },
-  );
-
-  app.post<{ Params: { id: string } }>('/api/v1/instances/:id/stop', async (request) => {
-    return service.stop(request.params.id);
-  });
-
-  app.post<{ Params: { id: string } }>('/api/v1/instances/:id/restart', async (request) => {
-    return service.restart(request.params.id);
+  app.delete<{ Params: { id: string } }>('/api/v1/instances/:id', async (request, reply) => {
+    const { serverId } = await service.remove(request.params.id);
+    // Reconcile: server will auto-create a replacement if replicas > 0
+    await service.reconcile(serverId);
+    reply.code(204);
   });
 
   app.get<{ Params: { id: string } }>('/api/v1/instances/:id/inspect', async (request) => {
     return service.inspect(request.params.id);
   });
 
-  app.delete<{ Params: { id: string } }>('/api/v1/instances/:id', async (request, reply) => {
-    await service.remove(request.params.id);
-    reply.code(204);
-  });
-
   app.get<{ Params: { id: string }; Querystring: { tail?: string } }>(
     '/api/v1/instances/:id/logs',
     async (request) => {

src/mcpd/src/routes/mcp-profiles.ts

@@ -1,27 +0,0 @@
-import type { FastifyInstance } from 'fastify';
-import type { McpProfileService } from '../services/mcp-profile.service.js';
-
-export function registerMcpProfileRoutes(app: FastifyInstance, service: McpProfileService): void {
-  app.get<{ Querystring: { serverId?: string } }>('/api/v1/profiles', async (request) => {
-    return service.list(request.query.serverId);
-  });
-
-  app.get<{ Params: { id: string } }>('/api/v1/profiles/:id', async (request) => {
-    return service.getById(request.params.id);
-  });
-
-  app.post('/api/v1/profiles', async (request, reply) => {
-    const profile = await service.create(request.body);
-    reply.code(201);
-    return profile;
-  });
-
-  app.put<{ Params: { id: string } }>('/api/v1/profiles/:id', async (request) => {
-    return service.update(request.params.id, request.body);
-  });
-
-  app.delete<{ Params: { id: string } }>('/api/v1/profiles/:id', async (request, reply) => {
-    await service.delete(request.params.id);
-    reply.code(204);
-  });
-}

src/mcpd/src/routes/mcp-servers.ts

@@ -1,7 +1,12 @@
 import type { FastifyInstance } from 'fastify';
 import type { McpServerService } from '../services/mcp-server.service.js';
+import type { InstanceService } from '../services/instance.service.js';
 
-export function registerMcpServerRoutes(app: FastifyInstance, service: McpServerService): void {
+export function registerMcpServerRoutes(
+  app: FastifyInstance,
+  service: McpServerService,
+  instanceService: InstanceService,
+): void {
   app.get('/api/v1/servers', async () => {
     return service.list();
   });
@@ -12,12 +17,17 @@ export function registerMcpServerRoutes(app: FastifyInstance, service: McpServer
 
   app.post('/api/v1/servers', async (request, reply) => {
     const server = await service.create(request.body);
+    // Auto-reconcile: create instances to match replicas
+    await instanceService.reconcile(server.id);
     reply.code(201);
     return server;
   });
 
   app.put<{ Params: { id: string } }>('/api/v1/servers/:id', async (request) => {
-    return service.update(request.params.id, request.body);
+    const server = await service.update(request.params.id, request.body);
+    // Re-reconcile after update (replicas may have changed)
+    await instanceService.reconcile(server.id);
+    return server;
   });
 
   app.delete<{ Params: { id: string } }>('/api/v1/servers/:id', async (request, reply) => {

src/mcpd/src/routes/projects.ts

@@ -26,18 +26,4 @@ export function registerProjectRoutes(app: FastifyInstance, service: ProjectServ
     await service.delete(request.params.id);
     reply.code(204);
   });
-
-  // Profile associations
-  app.get<{ Params: { id: string } }>('/api/v1/projects/:id/profiles', async (request) => {
-    return service.getProfiles(request.params.id);
-  });
-
-  app.put<{ Params: { id: string } }>('/api/v1/projects/:id/profiles', async (request) => {
-    return service.setProfiles(request.params.id, request.body);
-  });
-
-  // MCP config generation
-  app.get<{ Params: { id: string } }>('/api/v1/projects/:id/mcp-config', async (request) => {
-    return service.getMcpConfig(request.params.id);
-  });
 }

src/mcpd/src/routes/secrets.ts

@@ -0,0 +1,30 @@
+import type { FastifyInstance } from 'fastify';
+import type { SecretService } from '../services/secret.service.js';
+
+export function registerSecretRoutes(
+  app: FastifyInstance,
+  service: SecretService,
+): void {
+  app.get('/api/v1/secrets', async () => {
+    return service.list();
+  });
+
+  app.get<{ Params: { id: string } }>('/api/v1/secrets/:id', async (request) => {
+    return service.getById(request.params.id);
+  });
+
+  app.post('/api/v1/secrets', async (request, reply) => {
+    const secret = await service.create(request.body);
+    reply.code(201);
+    return secret;
+  });
+
+  app.put<{ Params: { id: string } }>('/api/v1/secrets/:id', async (request) => {
+    return service.update(request.params.id, request.body);
+  });
+
+  app.delete<{ Params: { id: string } }>('/api/v1/secrets/:id', async (request, reply) => {
+    await service.delete(request.params.id);
+    reply.code(204);
+  });
+}

src/mcpd/src/services/backup/backup-service.ts

@@ -1,4 +1,4 @@
-import type { IMcpServerRepository, IMcpProfileRepository } from '../../repositories/interfaces.js';
+import type { IMcpServerRepository, ISecretRepository } from '../../repositories/interfaces.js';
 import type { IProjectRepository } from '../../repositories/project.repository.js';
 import { encrypt, isSensitiveKey } from './crypto.js';
 import type { EncryptedPayload } from './crypto.js';
@@ -10,7 +10,7 @@ export interface BackupBundle {
   createdAt: string;
   encrypted: boolean;
   servers: BackupServer[];
-  profiles: BackupProfile[];
+  secrets: BackupSecret[];
   projects: BackupProject[];
   encryptedSecrets?: EncryptedPayload;
 }
@@ -22,39 +22,36 @@ export interface BackupServer {
   dockerImage: string | null;
   transport: string;
   repositoryUrl: string | null;
-  envTemplate: unknown;
+  env: unknown;
 }
 
-export interface BackupProfile {
+export interface BackupSecret {
   name: string;
-  serverName: string;
-  permissions: unknown;
-  envOverrides: unknown;
+  data: Record<string, string>;
 }
 
 export interface BackupProject {
   name: string;
   description: string;
-  profileNames: string[];
 }
 
 export interface BackupOptions {
   password?: string;
-  resources?: Array<'servers' | 'profiles' | 'projects'>;
+  resources?: Array<'servers' | 'secrets' | 'projects'>;
 }
 
 export class BackupService {
   constructor(
     private serverRepo: IMcpServerRepository,
-    private profileRepo: IMcpProfileRepository,
     private projectRepo: IProjectRepository,
+    private secretRepo: ISecretRepository,
   ) {}
 
   async createBackup(options?: BackupOptions): Promise<BackupBundle> {
-    const resources = options?.resources ?? ['servers', 'profiles', 'projects'];
+    const resources = options?.resources ?? ['servers', 'secrets', 'projects'];
 
     let servers: BackupServer[] = [];
-    let profiles: BackupProfile[] = [];
+    let secrets: BackupSecret[] = [];
     let projects: BackupProject[] = [];
 
     if (resources.includes('servers')) {
@@ -66,44 +63,24 @@ export class BackupService {
         dockerImage: s.dockerImage,
         transport: s.transport,
         repositoryUrl: s.repositoryUrl,
-        envTemplate: s.envTemplate,
+        env: s.env,
       }));
     }
 
-    if (resources.includes('profiles')) {
-      const allProfiles = await this.profileRepo.findAll();
-      const serverMap = new Map<string, string>();
-      const allServers = await this.serverRepo.findAll();
-      for (const s of allServers) {
-        serverMap.set(s.id, s.name);
-      }
-
-      profiles = allProfiles.map((p) => ({
-        name: p.name,
-        serverName: serverMap.get(p.serverId) ?? p.serverId,
-        permissions: p.permissions,
-        envOverrides: p.envOverrides,
+    if (resources.includes('secrets')) {
+      const allSecrets = await this.secretRepo.findAll();
+      secrets = allSecrets.map((s) => ({
+        name: s.name,
+        data: s.data as Record<string, string>,
       }));
     }
 
     if (resources.includes('projects')) {
       const allProjects = await this.projectRepo.findAll();
-      const allProfiles = await this.profileRepo.findAll();
-      const profileMap = new Map<string, string>();
-      for (const p of allProfiles) {
-        profileMap.set(p.id, p.name);
-      }
-
-      projects = await Promise.all(
-        allProjects.map(async (proj) => {
-          const profileIds = await this.projectRepo.getProfileIds(proj.id);
-          return {
-            name: proj.name,
-            description: proj.description,
-            profileNames: profileIds.map((id) => profileMap.get(id) ?? id),
-          };
-        }),
-      );
+      projects = allProjects.map((proj) => ({
+        name: proj.name,
+        description: proj.description,
+      }));
     }
 
     const bundle: BackupBundle = {
@@ -112,29 +89,26 @@ export class BackupService {
       createdAt: new Date().toISOString(),
       encrypted: false,
       servers,
-      profiles,
+      secrets,
       projects,
     };
 
-    if (options?.password) {
-      // Collect sensitive values and encrypt them
-      const secrets: Record<string, string> = {};
-      for (const profile of profiles) {
-        const overrides = profile.envOverrides as Record<string, string> | null;
-        if (overrides) {
-          for (const [key, value] of Object.entries(overrides)) {
-            if (isSensitiveKey(key)) {
-              const secretKey = `profile:${profile.name}:${key}`;
-              secrets[secretKey] = value;
-              (overrides as Record<string, string>)[key] = `__ENCRYPTED:${secretKey}__`;
-            }
+    if (options?.password && secrets.length > 0) {
+      // Collect sensitive values from secrets and encrypt them
+      const sensitiveData: Record<string, string> = {};
+      for (const secret of secrets) {
+        for (const [key, value] of Object.entries(secret.data)) {
+          if (isSensitiveKey(key)) {
+            const secretKey = `secret:${secret.name}:${key}`;
+            sensitiveData[secretKey] = value;
+            secret.data[key] = `__ENCRYPTED:${secretKey}__`;
           }
         }
       }
 
-      if (Object.keys(secrets).length > 0) {
+      if (Object.keys(sensitiveData).length > 0) {
         bundle.encrypted = true;
-        bundle.encryptedSecrets = encrypt(JSON.stringify(secrets), options.password);
+        bundle.encryptedSecrets = encrypt(JSON.stringify(sensitiveData), options.password);
       }
     }
 

src/mcpd/src/services/backup/index.ts

@@ -1,5 +1,5 @@
 export { BackupService } from './backup-service.js';
-export type { BackupBundle, BackupServer, BackupProfile, BackupProject, BackupOptions } from './backup-service.js';
+export type { BackupBundle, BackupServer, BackupSecret, BackupProject, BackupOptions } from './backup-service.js';
 export { RestoreService } from './restore-service.js';
 export type { RestoreOptions, RestoreResult, ConflictStrategy } from './restore-service.js';
 export { encrypt, decrypt, isSensitiveKey } from './crypto.js';

src/mcpd/src/services/backup/restore-service.ts

@@ -1,4 +1,4 @@
-import type { IMcpServerRepository, IMcpProfileRepository } from '../../repositories/interfaces.js';
+import type { IMcpServerRepository, ISecretRepository } from '../../repositories/interfaces.js';
 import type { IProjectRepository } from '../../repositories/project.repository.js';
 import { decrypt } from './crypto.js';
 import type { BackupBundle } from './backup-service.js';
@@ -13,8 +13,8 @@ export interface RestoreOptions {
 export interface RestoreResult {
   serversCreated: number;
   serversSkipped: number;
-  profilesCreated: number;
-  profilesSkipped: number;
+  secretsCreated: number;
+  secretsSkipped: number;
   projectsCreated: number;
   projectsSkipped: number;
   errors: string[];
@@ -23,8 +23,8 @@ export interface RestoreResult {
 export class RestoreService {
   constructor(
     private serverRepo: IMcpServerRepository,
-    private profileRepo: IMcpProfileRepository,
     private projectRepo: IProjectRepository,
+    private secretRepo: ISecretRepository,
   ) {}
 
   validateBundle(bundle: unknown): bundle is BackupBundle {
@@ -33,7 +33,7 @@ export class RestoreService {
     return (
       typeof b['version'] === 'string' &&
       Array.isArray(b['servers']) &&
-      Array.isArray(b['profiles']) &&
+      Array.isArray(b['secrets']) &&
       Array.isArray(b['projects'])
     );
   }
@@ -43,46 +43,42 @@ export class RestoreService {
     const result: RestoreResult = {
       serversCreated: 0,
       serversSkipped: 0,
-      profilesCreated: 0,
-      profilesSkipped: 0,
+      secretsCreated: 0,
+      secretsSkipped: 0,
       projectsCreated: 0,
       projectsSkipped: 0,
       errors: [],
     };
 
     // Decrypt secrets if encrypted
-    let secrets: Record<string, string> = {};
+    let decryptedSecrets: Record<string, string> = {};
     if (bundle.encrypted && bundle.encryptedSecrets) {
       if (!options?.password) {
         result.errors.push('Backup is encrypted but no password provided');
         return result;
       }
       try {
-        secrets = JSON.parse(decrypt(bundle.encryptedSecrets, options.password)) as Record<string, string>;
+        decryptedSecrets = JSON.parse(decrypt(bundle.encryptedSecrets, options.password)) as Record<string, string>;
       } catch {
         result.errors.push('Failed to decrypt backup - incorrect password or corrupted data');
         return result;
       }
     }
 
-    // Restore secrets into profile envOverrides
-    for (const profile of bundle.profiles) {
-      const overrides = profile.envOverrides as Record<string, string> | null;
-      if (overrides) {
-        for (const [key, value] of Object.entries(overrides)) {
-          if (typeof value === 'string' && value.startsWith('__ENCRYPTED:') && value.endsWith('__')) {
-            const secretKey = value.slice(12, -2);
-            const decrypted = secrets[secretKey];
-            if (decrypted !== undefined) {
-              overrides[key] = decrypted;
-            }
+    // Restore encrypted values into secret data
+    for (const secret of bundle.secrets) {
+      for (const [key, value] of Object.entries(secret.data)) {
+        if (typeof value === 'string' && value.startsWith('__ENCRYPTED:') && value.endsWith('__')) {
+          const secretKey = value.slice(12, -2);
+          const decrypted = decryptedSecrets[secretKey];
+          if (decrypted !== undefined) {
+            secret.data[key] = decrypted;
           }
         }
       }
     }
 
     // Restore servers
-    const serverNameToId = new Map<string, string>();
     for (const server of bundle.servers) {
       try {
         const existing = await this.serverRepo.findByName(server.name);
@@ -93,7 +89,6 @@ export class RestoreService {
           }
           if (strategy === 'skip') {
             result.serversSkipped++;
-            serverNameToId.set(server.name, existing.id);
             continue;
           }
           // overwrite
@@ -105,7 +100,6 @@ export class RestoreService {
           if (server.dockerImage) updateData.dockerImage = server.dockerImage;
           if (server.repositoryUrl) updateData.repositoryUrl = server.repositoryUrl;
           await this.serverRepo.update(existing.id, updateData);
-          serverNameToId.set(server.name, existing.id);
           result.serversCreated++;
           continue;
         }
@@ -114,66 +108,45 @@ export class RestoreService {
           name: server.name,
           description: server.description,
           transport: server.transport as 'STDIO' | 'SSE' | 'STREAMABLE_HTTP',
-          envTemplate: (server.envTemplate ?? []) as Array<{ name: string; description: string; isSecret: boolean }>,
+          replicas: (server as { replicas?: number }).replicas ?? 1,
+          env: (server.env ?? []) as Array<{ name: string; value?: string; valueFrom?: { secretRef: { name: string; key: string } } }>,
         };
         if (server.packageName) createData.packageName = server.packageName;
         if (server.dockerImage) createData.dockerImage = server.dockerImage;
         if (server.repositoryUrl) createData.repositoryUrl = server.repositoryUrl;
         const created = await this.serverRepo.create(createData);
-        serverNameToId.set(server.name, created.id);
         result.serversCreated++;
       } catch (err) {
         result.errors.push(`Failed to restore server "${server.name}": ${err instanceof Error ? err.message : String(err)}`);
       }
     }
 
-    // Restore profiles
-    const profileNameToId = new Map<string, string>();
-    for (const profile of bundle.profiles) {
+    // Restore secrets
+    for (const secret of bundle.secrets) {
       try {
-        const serverId = serverNameToId.get(profile.serverName);
-        if (!serverId) {
-          // Try to find server by name in DB
-          const server = await this.serverRepo.findByName(profile.serverName);
-          if (!server) {
-            result.errors.push(`Profile "${profile.name}" references unknown server "${profile.serverName}"`);
-            continue;
-          }
-          serverNameToId.set(profile.serverName, server.id);
-        }
-
-        const sid = serverNameToId.get(profile.serverName)!;
-        const existing = await this.profileRepo.findByServerAndName(sid, profile.name);
+        const existing = await this.secretRepo.findByName(secret.name);
         if (existing) {
           if (strategy === 'fail') {
-            result.errors.push(`Profile "${profile.name}" already exists for server "${profile.serverName}"`);
+            result.errors.push(`Secret "${secret.name}" already exists`);
             return result;
           }
           if (strategy === 'skip') {
-            result.profilesSkipped++;
-            profileNameToId.set(profile.name, existing.id);
+            result.secretsSkipped++;
             continue;
           }
           // overwrite
-          await this.profileRepo.update(existing.id, {
-            permissions: profile.permissions as string[],
-            envOverrides: profile.envOverrides as Record<string, string>,
-          });
-          profileNameToId.set(profile.name, existing.id);
-          result.profilesCreated++;
+          await this.secretRepo.update(existing.id, { data: secret.data });
+          result.secretsCreated++;
           continue;
         }
 
-        const created = await this.profileRepo.create({
-          name: profile.name,
-          serverId: sid,
-          permissions: profile.permissions as string[],
-          envOverrides: profile.envOverrides as Record<string, string>,
+        await this.secretRepo.create({
+          name: secret.name,
+          data: secret.data,
         });
-        profileNameToId.set(profile.name, created.id);
-        result.profilesCreated++;
+        result.secretsCreated++;
       } catch (err) {
-        result.errors.push(`Failed to restore profile "${profile.name}": ${err instanceof Error ? err.message : String(err)}`);
+        result.errors.push(`Failed to restore secret "${secret.name}": ${err instanceof Error ? err.message : String(err)}`);
       }
     }
 
@@ -190,29 +163,17 @@ export class RestoreService {
             result.projectsSkipped++;
             continue;
           }
-          // overwrite - update and set profiles
+          // overwrite
           await this.projectRepo.update(existing.id, { description: project.description });
-          const profileIds = project.profileNames
-            .map((name) => profileNameToId.get(name))
-            .filter((id): id is string => id !== undefined);
-          if (profileIds.length > 0) {
-            await this.projectRepo.setProfiles(existing.id, profileIds);
-          }
           result.projectsCreated++;
           continue;
         }
 
-        const created = await this.projectRepo.create({
+        await this.projectRepo.create({
           name: project.name,
           description: project.description,
           ownerId: 'system',
         });
-        const profileIds = project.profileNames
-          .map((name) => profileNameToId.get(name))
-          .filter((id): id is string => id !== undefined);
-        if (profileIds.length > 0) {
-          await this.projectRepo.setProfiles(created.id, profileIds);
-        }
         result.projectsCreated++;
       } catch (err) {
         result.errors.push(`Failed to restore project "${project.name}": ${err instanceof Error ? err.message : String(err)}`);

src/mcpd/src/services/docker/container-manager.ts

@@ -74,7 +74,7 @@ export class DockerContainerManager implements McpOrchestrator {
       ? Object.entries(spec.env).map(([k, v]) => `${k}=${v}`)
       : undefined;
 
-    const container = await this.docker.createContainer({
+    const createOpts: Docker.ContainerCreateOptions = {
       Image: spec.image,
       name: spec.name,
       Env: envArr,
@@ -86,7 +86,12 @@ export class DockerContainerManager implements McpOrchestrator {
         NanoCpus: nanoCpus,
         NetworkMode: spec.network ?? 'bridge',
       },
-    });
+    };
+    if (spec.command) {
+      createOpts.Cmd = spec.command;
+    }
+
+    const container = await this.docker.createContainer(createOpts);
 
     await container.start();
 

src/mcpd/src/services/env-resolver.ts

@@ -0,0 +1,44 @@
+import type { McpServer } from '@prisma/client';
+import type { ISecretRepository } from '../repositories/interfaces.js';
+import type { ServerEnvEntry } from '../validation/mcp-server.schema.js';
+
+/**
+ * Resolve a server's env entries into a flat key-value map.
+ * - Inline `value` entries are used directly.
+ * - `valueFrom.secretRef` entries are looked up from the secret repository.
+ * Throws if a referenced secret or key is missing.
+ */
+export async function resolveServerEnv(
+  server: McpServer,
+  secretRepo: ISecretRepository,
+): Promise<Record<string, string>> {
+  const entries = server.env as ServerEnvEntry[];
+  if (!entries || entries.length === 0) return {};
+
+  const result: Record<string, string> = {};
+  const secretCache = new Map<string, Record<string, string>>();
+
+  for (const entry of entries) {
+    if (entry.value !== undefined) {
+      result[entry.name] = entry.value;
+    } else if (entry.valueFrom?.secretRef) {
+      const { name: secretName, key } = entry.valueFrom.secretRef;
+
+      if (!secretCache.has(secretName)) {
+        const secret = await secretRepo.findByName(secretName);
+        if (!secret) {
+          throw new Error(`Secret '${secretName}' not found (referenced by server '${server.name}' env '${entry.name}')`);
+        }
+        secretCache.set(secretName, secret.data as Record<string, string>);
+      }
+
+      const data = secretCache.get(secretName)!;
+      if (!(key in data)) {
+        throw new Error(`Key '${key}' not found in secret '${secretName}' (referenced by server '${server.name}' env '${entry.name}')`);
+      }
+      result[entry.name] = data[key]!;
+    }
+  }
+
+  return result;
+}

src/mcpd/src/services/index.ts

@@ -1,9 +1,10 @@
 export { McpServerService, NotFoundError, ConflictError } from './mcp-server.service.js';
-export { McpProfileService } from './mcp-profile.service.js';
+export { SecretService } from './secret.service.js';
+export { resolveServerEnv } from './env-resolver.js';
 export { ProjectService } from './project.service.js';
 export { InstanceService, InvalidStateError } from './instance.service.js';
 export { generateMcpConfig } from './mcp-config-generator.js';
-export type { McpConfig, McpConfigServer, ProfileWithServer } from './mcp-config-generator.js';
+export type { McpConfig, McpConfigServer } from './mcp-config-generator.js';
 export type { McpOrchestrator, ContainerSpec, ContainerInfo, ContainerLogs } from './orchestrator.js';
 export { DEFAULT_MEMORY_LIMIT, DEFAULT_NANO_CPUS } from './orchestrator.js';
 export { DockerContainerManager } from './docker/container-manager.js';

src/mcpd/src/services/instance.service.ts

@@ -1,7 +1,8 @@
 import type { McpInstance } from '@prisma/client';
-import type { IMcpInstanceRepository, IMcpServerRepository } from '../repositories/interfaces.js';
+import type { IMcpInstanceRepository, IMcpServerRepository, ISecretRepository } from '../repositories/interfaces.js';
 import type { McpOrchestrator, ContainerSpec, ContainerInfo } from './orchestrator.js';
 import { NotFoundError } from './mcp-server.service.js';
+import { resolveServerEnv } from './env-resolver.js';
 
 export class InvalidStateError extends Error {
   readonly statusCode = 409;
@@ -16,6 +17,7 @@ export class InstanceService {
     private instanceRepo: IMcpInstanceRepository,
     private serverRepo: IMcpServerRepository,
     private orchestrator: McpOrchestrator,
+    private secretRepo?: ISecretRepository,
   ) {}
 
   async list(serverId?: string): Promise<McpInstance[]> {
@@ -28,81 +30,46 @@ export class InstanceService {
     return instance;
   }
 
-  async start(serverId: string, opts?: { env?: Record<string, string>; hostPort?: number }): Promise<McpInstance> {
+  /**
+   * Reconcile instances for a server to match desired replica count.
+   * - If fewer running instances than replicas: start new ones
+   * - If more running instances than replicas: remove excess (oldest first)
+   */
+  async reconcile(serverId: string): Promise<McpInstance[]> {
     const server = await this.serverRepo.findById(serverId);
     if (!server) throw new NotFoundError(`McpServer '${serverId}' not found`);
 
-    const image = server.dockerImage ?? server.packageName ?? server.name;
+    const instances = await this.instanceRepo.findAll(serverId);
+    const active = instances.filter((i) => i.status === 'RUNNING' || i.status === 'STARTING');
+    const desired = server.replicas;
 
-    // Create DB record first in STARTING state
-    let instance = await this.instanceRepo.create({
-      serverId,
-      status: 'STARTING',
-    });
-
-    try {
-      const spec: ContainerSpec = {
-        image,
-        name: `mcpctl-${server.name}-${instance.id}`,
-        hostPort: opts?.hostPort ?? null,
-        labels: {
-          'mcpctl.server-id': serverId,
-          'mcpctl.instance-id': instance.id,
-        },
-      };
-      if (server.transport === 'SSE' || server.transport === 'STREAMABLE_HTTP') {
-        spec.containerPort = 3000;
+    if (active.length < desired) {
+      // Scale up
+      const toStart = desired - active.length;
+      for (let i = 0; i < toStart; i++) {
+        await this.startOne(serverId);
       }
-      if (opts?.env) {
-        spec.env = opts.env;
+    } else if (active.length > desired) {
+      // Scale down — remove oldest first
+      const excess = active
+        .sort((a, b) => a.createdAt.getTime() - b.createdAt.getTime())
+        .slice(0, active.length - desired);
+      for (const inst of excess) {
+        await this.removeOne(inst);
       }
-
-      const containerInfo = await this.orchestrator.createContainer(spec);
-
-      const updateFields: { containerId: string; port?: number } = {
-        containerId: containerInfo.containerId,
-      };
-      if (containerInfo.port !== undefined) {
-        updateFields.port = containerInfo.port;
-      }
-
-      instance = await this.instanceRepo.updateStatus(instance.id, 'RUNNING', updateFields);
-    } catch (err) {
-      // Mark as ERROR if container creation fails
-      instance = await this.instanceRepo.updateStatus(instance.id, 'ERROR', {
-        metadata: { error: err instanceof Error ? err.message : String(err) },
-      });
     }
 
-    return instance;
+    return this.instanceRepo.findAll(serverId);
   }
 
-  async stop(id: string): Promise<McpInstance> {
-    const instance = await this.getById(id);
-    if (instance.status === 'STOPPED') {
-      throw new InvalidStateError(`Instance '${id}' is already stopped`);
-    }
-    if (!instance.containerId) {
-      return this.instanceRepo.updateStatus(id, 'STOPPED');
-    }
-
-    await this.instanceRepo.updateStatus(id, 'STOPPING');
-
-    try {
-      await this.orchestrator.stopContainer(instance.containerId);
-      return await this.instanceRepo.updateStatus(id, 'STOPPED');
-    } catch (err) {
-      return await this.instanceRepo.updateStatus(id, 'ERROR', {
-        metadata: { error: err instanceof Error ? err.message : String(err) },
-      });
-    }
-  }
-
-  async restart(id: string): Promise<McpInstance> {
+  /**
+   * Remove an instance (stop container + delete DB record).
+   * Does NOT reconcile — caller should reconcile after if needed.
+   */
+  async remove(id: string): Promise<{ serverId: string }> {
     const instance = await this.getById(id);
 
-    // Stop if running
-    if (instance.containerId && (instance.status === 'RUNNING' || instance.status === 'STARTING')) {
+    if (instance.containerId) {
       try {
         await this.orchestrator.stopContainer(instance.containerId);
       } catch {
@@ -116,9 +83,29 @@ export class InstanceService {
     }
 
     await this.instanceRepo.delete(id);
+    return { serverId: instance.serverId };
+  }
 
-    // Start a fresh instance for the same server
-    return this.start(instance.serverId);
+  /**
+   * Remove all instances for a server (used before server deletion).
+   * Stops all containers so Prisma cascade only cleans up DB records.
+   */
+  async removeAllForServer(serverId: string): Promise<void> {
+    const instances = await this.instanceRepo.findAll(serverId);
+    for (const inst of instances) {
+      if (inst.containerId) {
+        try {
+          await this.orchestrator.stopContainer(inst.containerId);
+        } catch {
+          // best-effort
+        }
+        try {
+          await this.orchestrator.removeContainer(inst.containerId, true);
+        } catch {
+          // best-effort
+        }
+      }
+    }
   }
 
   async inspect(id: string): Promise<ContainerInfo> {
@@ -129,20 +116,6 @@ export class InstanceService {
     return this.orchestrator.inspectContainer(instance.containerId);
   }
 
-  async remove(id: string): Promise<void> {
-    const instance = await this.getById(id);
-
-    if (instance.containerId) {
-      try {
-        await this.orchestrator.removeContainer(instance.containerId, true);
-      } catch {
-        // Container may already be gone, proceed with DB cleanup
-      }
-    }
-
-    await this.instanceRepo.delete(id);
-  }
-
   async getLogs(id: string, opts?: { tail?: number }): Promise<{ stdout: string; stderr: string }> {
     const instance = await this.getById(id);
     if (!instance.containerId) {
@@ -151,4 +124,88 @@ export class InstanceService {
 
     return this.orchestrator.getContainerLogs(instance.containerId, opts);
   }
+
+  /** Start a single instance for a server. */
+  private async startOne(serverId: string): Promise<McpInstance> {
+    const server = await this.serverRepo.findById(serverId);
+    if (!server) throw new NotFoundError(`McpServer '${serverId}' not found`);
+
+    // External servers don't need container management
+    if (server.externalUrl) {
+      return this.instanceRepo.create({
+        serverId,
+        status: 'RUNNING',
+        metadata: { external: true, url: server.externalUrl },
+      });
+    }
+
+    const image = server.dockerImage ?? server.packageName ?? server.name;
+
+    let instance = await this.instanceRepo.create({
+      serverId,
+      status: 'STARTING',
+    });
+
+    try {
+      const spec: ContainerSpec = {
+        image,
+        name: `mcpctl-${server.name}-${instance.id}`,
+        hostPort: null,
+        labels: {
+          'mcpctl.server-id': serverId,
+          'mcpctl.instance-id': instance.id,
+        },
+      };
+      if (server.transport === 'SSE' || server.transport === 'STREAMABLE_HTTP') {
+        spec.containerPort = server.containerPort ?? 3000;
+      }
+      const command = server.command as string[] | null;
+      if (command) {
+        spec.command = command;
+      }
+
+      // Resolve env vars from inline values and secret refs
+      if (this.secretRepo) {
+        try {
+          const resolvedEnv = await resolveServerEnv(server, this.secretRepo);
+          if (Object.keys(resolvedEnv).length > 0) {
+            spec.env = resolvedEnv;
+          }
+        } catch (envErr) {
+          // Log but don't prevent startup — env resolution failures are non-fatal
+          // The container may still work if env vars are optional
+        }
+      }
+
+      const containerInfo = await this.orchestrator.createContainer(spec);
+
+      const updateFields: { containerId: string; port?: number } = {
+        containerId: containerInfo.containerId,
+      };
+      if (containerInfo.port !== undefined) {
+        updateFields.port = containerInfo.port;
+      }
+
+      instance = await this.instanceRepo.updateStatus(instance.id, 'RUNNING', updateFields);
+    } catch (err) {
+      instance = await this.instanceRepo.updateStatus(instance.id, 'ERROR', {
+        metadata: { error: err instanceof Error ? err.message : String(err) },
+      });
+    }
+
+    return instance;
+  }
+
+  /** Stop and remove a single instance. */
+  private async removeOne(instance: McpInstance): Promise<void> {
+    if (instance.containerId) {
+      try {
+        await this.orchestrator.stopContainer(instance.containerId);
+      } catch { /* best-effort */ }
+      try {
+        await this.orchestrator.removeContainer(instance.containerId, true);
+      } catch { /* best-effort */ }
+    }
+    await this.instanceRepo.delete(instance.id);
+  }
 }

src/mcpd/src/services/mcp-config-generator.ts

@@ -1,4 +1,4 @@
-import type { McpServer, McpProfile } from '@prisma/client';
+import type { McpServer } from '@prisma/client';
 
 export interface McpConfigServer {
   command: string;
@@ -10,49 +10,25 @@ export interface McpConfig {
   mcpServers: Record<string, McpConfigServer>;
 }
 
-export interface ProfileWithServer {
-  profile: McpProfile;
-  server: McpServer;
-}
-
 /**
- * Generate .mcp.json config from a project's profiles.
- * Secret env vars are excluded from the output — they must be injected at runtime.
+ * Generate .mcp.json config from servers with their resolved env vars.
  */
-export function generateMcpConfig(profiles: ProfileWithServer[]): McpConfig {
+export function generateMcpConfig(
+  servers: Array<{ server: McpServer; resolvedEnv: Record<string, string> }>,
+): McpConfig {
   const mcpServers: Record<string, McpConfigServer> = {};
 
-  for (const { profile, server } of profiles) {
-    const key = `${server.name}--${profile.name}`;
-    const envTemplate = server.envTemplate as Array<{
-      name: string;
-      isSecret: boolean;
-      defaultValue?: string;
-    }>;
-    const envOverrides = profile.envOverrides as Record<string, string>;
-
-    // Build env: only include non-secret env vars
-    const env: Record<string, string> = {};
-    for (const entry of envTemplate) {
-      if (entry.isSecret) continue; // Never include secrets in config output
-      const override = envOverrides[entry.name];
-      if (override !== undefined) {
-        env[entry.name] = override;
-      } else if (entry.defaultValue !== undefined) {
-        env[entry.name] = entry.defaultValue;
-      }
-    }
-
+  for (const { server, resolvedEnv } of servers) {
     const config: McpConfigServer = {
       command: 'npx',
       args: ['-y', server.packageName ?? server.name],
     };
 
-    if (Object.keys(env).length > 0) {
-      config.env = env;
+    if (Object.keys(resolvedEnv).length > 0) {
+      config.env = resolvedEnv;
     }
 
-    mcpServers[key] = config;
+    mcpServers[server.name] = config;
   }
 
   return { mcpServers };

src/mcpd/src/services/mcp-profile.service.ts

@@ -1,62 +0,0 @@
-import type { McpProfile } from '@prisma/client';
-import type { IMcpProfileRepository, IMcpServerRepository } from '../repositories/interfaces.js';
-import { CreateMcpProfileSchema, UpdateMcpProfileSchema } from '../validation/mcp-profile.schema.js';
-import { NotFoundError, ConflictError } from './mcp-server.service.js';
-
-export class McpProfileService {
-  constructor(
-    private readonly profileRepo: IMcpProfileRepository,
-    private readonly serverRepo: IMcpServerRepository,
-  ) {}
-
-  async list(serverId?: string): Promise<McpProfile[]> {
-    return this.profileRepo.findAll(serverId);
-  }
-
-  async getById(id: string): Promise<McpProfile> {
-    const profile = await this.profileRepo.findById(id);
-    if (profile === null) {
-      throw new NotFoundError(`Profile not found: ${id}`);
-    }
-    return profile;
-  }
-
-  async create(input: unknown): Promise<McpProfile> {
-    const data = CreateMcpProfileSchema.parse(input);
-
-    // Verify server exists
-    const server = await this.serverRepo.findById(data.serverId);
-    if (server === null) {
-      throw new NotFoundError(`Server not found: ${data.serverId}`);
-    }
-
-    // Check unique name per server
-    const existing = await this.profileRepo.findByServerAndName(data.serverId, data.name);
-    if (existing !== null) {
-      throw new ConflictError(`Profile "${data.name}" already exists for server "${server.name}"`);
-    }
-
-    return this.profileRepo.create(data);
-  }
-
-  async update(id: string, input: unknown): Promise<McpProfile> {
-    const data = UpdateMcpProfileSchema.parse(input);
-
-    const profile = await this.getById(id);
-
-    // If renaming, check uniqueness
-    if (data.name !== undefined && data.name !== profile.name) {
-      const existing = await this.profileRepo.findByServerAndName(profile.serverId, data.name);
-      if (existing !== null) {
-        throw new ConflictError(`Profile "${data.name}" already exists for this server`);
-      }
-    }
-
-    return this.profileRepo.update(id, data);
-  }
-
-  async delete(id: string): Promise<void> {
-    await this.getById(id);
-    await this.profileRepo.delete(id);
-  }
-}

src/mcpd/src/services/mcp-proxy-service.ts

@@ -1,5 +1,5 @@
 import type { McpInstance } from '@prisma/client';
-import type { IMcpInstanceRepository } from '../repositories/interfaces.js';
+import type { IMcpInstanceRepository, IMcpServerRepository } from '../repositories/interfaces.js';
 import { NotFoundError } from './mcp-server.service.js';
 import { InvalidStateError } from './instance.service.js';
 
@@ -16,11 +16,39 @@ export interface McpProxyResponse {
   error?: { code: number; message: string; data?: unknown };
 }
 
+/**
+ * Parses a streamable-http SSE response body to extract the JSON-RPC payload.
+ * Streamable-http returns `event: message\ndata: {...}\n\n` format.
+ */
+function parseStreamableResponse(body: string): McpProxyResponse {
+  for (const line of body.split('\n')) {
+    const trimmed = line.trim();
+    if (trimmed.startsWith('data: ')) {
+      return JSON.parse(trimmed.slice(6)) as McpProxyResponse;
+    }
+  }
+  // If body is plain JSON (no SSE framing), parse directly
+  return JSON.parse(body) as McpProxyResponse;
+}
+
 export class McpProxyService {
-  constructor(private readonly instanceRepo: IMcpInstanceRepository) {}
+  /** Session IDs per server for streamable-http protocol */
+  private sessions = new Map<string, string>();
+
+  constructor(
+    private readonly instanceRepo: IMcpInstanceRepository,
+    private readonly serverRepo: IMcpServerRepository,
+  ) {}
 
   async execute(request: McpProxyRequest): Promise<McpProxyResponse> {
-    // Find a running instance for this server
+    const server = await this.serverRepo.findById(request.serverId);
+
+    // External server: proxy directly to externalUrl
+    if (server?.externalUrl) {
+      return this.sendToExternal(server.id, server.externalUrl, request.method, request.params);
+    }
+
+    // Managed server: find running instance
     const instances = await this.instanceRepo.findAll(request.serverId);
     const running = instances.find((i) => i.status === 'RUNNING');
 
@@ -37,6 +65,116 @@ export class McpProxyService {
     return this.sendJsonRpc(running, request.method, request.params);
   }
 
+  /**
+   * Send a JSON-RPC request to an external MCP server.
+   * Handles streamable-http protocol (session management + SSE response parsing).
+   */
+  private async sendToExternal(
+    serverId: string,
+    url: string,
+    method: string,
+    params?: Record<string, unknown>,
+  ): Promise<McpProxyResponse> {
+    // Ensure we have a session (initialize on first call)
+    if (!this.sessions.has(serverId)) {
+      await this.initSession(serverId, url);
+    }
+
+    const sessionId = this.sessions.get(serverId);
+
+    const body: Record<string, unknown> = {
+      jsonrpc: '2.0',
+      id: 1,
+      method,
+    };
+    if (params !== undefined) {
+      body.params = params;
+    }
+
+    const headers: Record<string, string> = {
+      'Content-Type': 'application/json',
+      'Accept': 'application/json, text/event-stream',
+    };
+    if (sessionId) {
+      headers['Mcp-Session-Id'] = sessionId;
+    }
+
+    const response = await fetch(url, {
+      method: 'POST',
+      headers,
+      body: JSON.stringify(body),
+    });
+
+    if (!response.ok) {
+      // Session expired? Clear and retry once
+      if (response.status === 400 || response.status === 404) {
+        this.sessions.delete(serverId);
+        return this.sendToExternal(serverId, url, method, params);
+      }
+      return {
+        jsonrpc: '2.0',
+        id: 1,
+        error: {
+          code: -32000,
+          message: `External MCP server returned HTTP ${response.status}: ${response.statusText}`,
+        },
+      };
+    }
+
+    const text = await response.text();
+    return parseStreamableResponse(text);
+  }
+
+  /**
+   * Initialize a streamable-http session with an external server.
+   * Sends `initialize` and `notifications/initialized`, caches the session ID.
+   */
+  private async initSession(serverId: string, url: string): Promise<void> {
+    const initBody = {
+      jsonrpc: '2.0',
+      id: 1,
+      method: 'initialize',
+      params: {
+        protocolVersion: '2025-03-26',
+        capabilities: {},
+        clientInfo: { name: 'mcpctl', version: '0.1.0' },
+      },
+    };
+
+    const response = await fetch(url, {
+      method: 'POST',
+      headers: {
+        'Content-Type': 'application/json',
+        'Accept': 'application/json, text/event-stream',
+      },
+      body: JSON.stringify(initBody),
+    });
+
+    if (!response.ok) {
+      throw new Error(`Failed to initialize session: HTTP ${response.status}`);
+    }
+
+    const sessionId = response.headers.get('mcp-session-id');
+    if (sessionId) {
+      this.sessions.set(serverId, sessionId);
+    }
+
+    // Send notifications/initialized
+    const headers: Record<string, string> = {
+      'Content-Type': 'application/json',
+      'Accept': 'application/json, text/event-stream',
+    };
+    if (sessionId) {
+      headers['Mcp-Session-Id'] = sessionId;
+    }
+
+    await fetch(url, {
+      method: 'POST',
+      headers,
+      body: JSON.stringify({ jsonrpc: '2.0', method: 'notifications/initialized' }),
+    });
+  }
+
   private async sendJsonRpc(
     instance: McpInstance,
     method: string,

src/mcpd/src/services/mcp-server.service.ts

@@ -1,10 +1,18 @@
 import type { McpServer } from '@prisma/client';
 import type { IMcpServerRepository } from '../repositories/interfaces.js';
+import type { InstanceService } from './instance.service.js';
 import { CreateMcpServerSchema, UpdateMcpServerSchema } from '../validation/mcp-server.schema.js';
 
 export class McpServerService {
+  private instanceService: InstanceService | null = null;
+
   constructor(private readonly repo: IMcpServerRepository) {}
 
+  /** Set after construction to avoid circular dependency. */
+  setInstanceService(instanceService: InstanceService): void {
+    this.instanceService = instanceService;
+  }
+
   async list(): Promise<McpServer[]> {
     return this.repo.findAll();
   }
@@ -48,6 +56,10 @@ export class McpServerService {
   async delete(id: string): Promise<void> {
     // Verify exists
     await this.getById(id);
+    // Stop all containers before DB cascade
+    if (this.instanceService) {
+      await this.instanceService.removeAllForServer(id);
+    }
     await this.repo.delete(id);
   }
 }

src/mcpd/src/services/orchestrator.ts

@@ -7,6 +7,8 @@ export interface ContainerSpec {
   image: string;
   /** Human-readable name (used as container name prefix) */
   name: string;
+  /** Custom command to run (overrides image CMD) */
+  command?: string[];
   /** Environment variables */
   env?: Record<string, string>;
   /** Host port to bind (null = auto-assign) */

src/mcpd/src/services/project.service.ts

@@ -1,15 +1,12 @@
 import type { Project } from '@prisma/client';
 import type { IProjectRepository } from '../repositories/project.repository.js';
-import type { IMcpProfileRepository, IMcpServerRepository } from '../repositories/interfaces.js';
-import { CreateProjectSchema, UpdateProjectSchema, UpdateProjectProfilesSchema } from '../validation/project.schema.js';
+import type { IMcpServerRepository } from '../repositories/interfaces.js';
+import { CreateProjectSchema, UpdateProjectSchema } from '../validation/project.schema.js';
 import { NotFoundError, ConflictError } from './mcp-server.service.js';
-import { generateMcpConfig } from './mcp-config-generator.js';
-import type { McpConfig, ProfileWithServer } from './mcp-config-generator.js';
 
 export class ProjectService {
   constructor(
     private readonly projectRepo: IProjectRepository,
-    private readonly profileRepo: IMcpProfileRepository,
     private readonly serverRepo: IMcpServerRepository,
   ) {}
 
@@ -46,41 +43,4 @@ export class ProjectService {
     await this.getById(id);
     await this.projectRepo.delete(id);
   }
-
-  async setProfiles(projectId: string, input: unknown): Promise<string[]> {
-    const { profileIds } = UpdateProjectProfilesSchema.parse(input);
-    await this.getById(projectId);
-
-    // Verify all profiles exist
-    for (const profileId of profileIds) {
-      const profile = await this.profileRepo.findById(profileId);
-      if (profile === null) {
-        throw new NotFoundError(`Profile not found: ${profileId}`);
-      }
-    }
-
-    await this.projectRepo.setProfiles(projectId, profileIds);
-    return profileIds;
-  }
-
-  async getProfiles(projectId: string): Promise<string[]> {
-    await this.getById(projectId);
-    return this.projectRepo.getProfileIds(projectId);
-  }
-
-  async getMcpConfig(projectId: string): Promise<McpConfig> {
-    await this.getById(projectId);
-    const profileIds = await this.projectRepo.getProfileIds(projectId);
-
-    const profilesWithServers: ProfileWithServer[] = [];
-    for (const profileId of profileIds) {
-      const profile = await this.profileRepo.findById(profileId);
-      if (profile === null) continue;
-      const server = await this.serverRepo.findById(profile.serverId);
-      if (server === null) continue;
-      profilesWithServers.push({ profile, server });
-    }
-
-    return generateMcpConfig(profilesWithServers);
-  }
 }

src/mcpd/src/services/secret.service.ts

@@ -0,0 +1,54 @@
+import type { Secret } from '@prisma/client';
+import type { ISecretRepository } from '../repositories/interfaces.js';
+import { CreateSecretSchema, UpdateSecretSchema } from '../validation/secret.schema.js';
+import { NotFoundError, ConflictError } from './mcp-server.service.js';
+
+export class SecretService {
+  constructor(private readonly repo: ISecretRepository) {}
+
+  async list(): Promise<Secret[]> {
+    return this.repo.findAll();
+  }
+
+  async getById(id: string): Promise<Secret> {
+    const secret = await this.repo.findById(id);
+    if (secret === null) {
+      throw new NotFoundError(`Secret not found: ${id}`);
+    }
+    return secret;
+  }
+
+  async getByName(name: string): Promise<Secret> {
+    const secret = await this.repo.findByName(name);
+    if (secret === null) {
+      throw new NotFoundError(`Secret not found: ${name}`);
+    }
+    return secret;
+  }
+
+  async create(input: unknown): Promise<Secret> {
+    const data = CreateSecretSchema.parse(input);
+
+    const existing = await this.repo.findByName(data.name);
+    if (existing !== null) {
+      throw new ConflictError(`Secret already exists: ${data.name}`);
+    }
+
+    return this.repo.create(data);
+  }
+
+  async update(id: string, input: unknown): Promise<Secret> {
+    const data = UpdateSecretSchema.parse(input);
+
+    // Verify exists
+    await this.getById(id);
+
+    return this.repo.update(id, data);
+  }
+
+  async delete(id: string): Promise<void> {
+    // Verify exists
+    await this.getById(id);
+    await this.repo.delete(id);
+  }
+}

src/mcpd/src/validation/index.ts

@@ -1,6 +1,4 @@
 export { CreateMcpServerSchema, UpdateMcpServerSchema } from './mcp-server.schema.js';
 export type { CreateMcpServerInput, UpdateMcpServerInput } from './mcp-server.schema.js';
-export { CreateMcpProfileSchema, UpdateMcpProfileSchema } from './mcp-profile.schema.js';
-export type { CreateMcpProfileInput, UpdateMcpProfileInput } from './mcp-profile.schema.js';
-export { CreateProjectSchema, UpdateProjectSchema, UpdateProjectProfilesSchema } from './project.schema.js';
-export type { CreateProjectInput, UpdateProjectInput, UpdateProjectProfilesInput } from './project.schema.js';
+export { CreateProjectSchema, UpdateProjectSchema } from './project.schema.js';
+export type { CreateProjectInput, UpdateProjectInput } from './project.schema.js';

src/mcpd/src/validation/mcp-profile.schema.ts

@@ -1,17 +0,0 @@
-import { z } from 'zod';
-
-export const CreateMcpProfileSchema = z.object({
-  name: z.string().min(1).max(100).regex(/^[a-z0-9-]+$/, 'Name must be lowercase alphanumeric with hyphens'),
-  serverId: z.string().min(1),
-  permissions: z.array(z.string()).default([]),
-  envOverrides: z.record(z.string()).default({}),
-});
-
-export const UpdateMcpProfileSchema = z.object({
-  name: z.string().min(1).max(100).regex(/^[a-z0-9-]+$/).optional(),
-  permissions: z.array(z.string()).optional(),
-  envOverrides: z.record(z.string()).optional(),
-});
-
-export type CreateMcpProfileInput = z.infer<typeof CreateMcpProfileSchema>;
-export type UpdateMcpProfileInput = z.infer<typeof UpdateMcpProfileSchema>;

src/mcpd/src/validation/mcp-server.schema.ts

@@ -1,12 +1,23 @@
 import { z } from 'zod';
 
-const EnvTemplateEntrySchema = z.object({
-  name: z.string().min(1).max(100),
-  description: z.string().max(500).default(''),
-  isSecret: z.boolean().default(false),
-  setupUrl: z.string().url().optional(),
+const SecretRefSchema = z.object({
+  name: z.string().min(1),
+  key: z.string().min(1),
 });
 
+export const ServerEnvEntrySchema = z.object({
+  name: z.string().min(1).max(100),
+  value: z.string().optional(),
+  valueFrom: z.object({
+    secretRef: SecretRefSchema,
+  }).optional(),
+}).refine(
+  (e) => (e.value !== undefined) !== (e.valueFrom !== undefined),
+  { message: 'Exactly one of value or valueFrom must be set' },
+);
+
+export type ServerEnvEntry = z.infer<typeof ServerEnvEntrySchema>;
+
 export const CreateMcpServerSchema = z.object({
   name: z.string().min(1).max(100).regex(/^[a-z0-9-]+$/, 'Name must be lowercase alphanumeric with hyphens'),
   description: z.string().max(1000).default(''),
@@ -14,7 +25,11 @@ export const CreateMcpServerSchema = z.object({
   dockerImage: z.string().max(200).optional(),
   transport: z.enum(['STDIO', 'SSE', 'STREAMABLE_HTTP']).default('STDIO'),
   repositoryUrl: z.string().url().optional(),
-  envTemplate: z.array(EnvTemplateEntrySchema).default([]),
+  externalUrl: z.string().url().optional(),
+  command: z.array(z.string()).optional(),
+  containerPort: z.number().int().min(1).max(65535).optional(),
+  replicas: z.number().int().min(0).max(10).default(1),
+  env: z.array(ServerEnvEntrySchema).default([]),
 });
 
 export const UpdateMcpServerSchema = z.object({
@@ -23,7 +38,11 @@ export const UpdateMcpServerSchema = z.object({
   dockerImage: z.string().max(200).nullable().optional(),
   transport: z.enum(['STDIO', 'SSE', 'STREAMABLE_HTTP']).optional(),
   repositoryUrl: z.string().url().nullable().optional(),
-  envTemplate: z.array(EnvTemplateEntrySchema).optional(),
+  externalUrl: z.string().url().nullable().optional(),
+  command: z.array(z.string()).nullable().optional(),
+  containerPort: z.number().int().min(1).max(65535).nullable().optional(),
+  replicas: z.number().int().min(0).max(10).optional(),
+  env: z.array(ServerEnvEntrySchema).optional(),
 });
 
 export type CreateMcpServerInput = z.infer<typeof CreateMcpServerSchema>;

src/mcpd/src/validation/project.schema.ts

@@ -9,10 +9,5 @@ export const UpdateProjectSchema = z.object({
   description: z.string().max(1000).optional(),
 });
 
-export const UpdateProjectProfilesSchema = z.object({
-  profileIds: z.array(z.string().min(1)).min(0),
-});
-
 export type CreateProjectInput = z.infer<typeof CreateProjectSchema>;
 export type UpdateProjectInput = z.infer<typeof UpdateProjectSchema>;
-export type UpdateProjectProfilesInput = z.infer<typeof UpdateProjectProfilesSchema>;

src/mcpd/src/validation/secret.schema.ts

@@ -0,0 +1,13 @@
+import { z } from 'zod';
+
+export const CreateSecretSchema = z.object({
+  name: z.string().min(1).max(100).regex(/^[a-z0-9-]+$/, 'Name must be lowercase alphanumeric with hyphens'),
+  data: z.record(z.string()).default({}),
+});
+
+export const UpdateSecretSchema = z.object({
+  data: z.record(z.string()),
+});
+
+export type CreateSecretInput = z.infer<typeof CreateSecretSchema>;
+export type UpdateSecretInput = z.infer<typeof UpdateSecretSchema>;

src/mcpd/tests/backup.test.ts

@@ -4,7 +4,7 @@ import { BackupService } from '../src/services/backup/backup-service.js';
 import { RestoreService } from '../src/services/backup/restore-service.js';
 import { encrypt, decrypt, isSensitiveKey } from '../src/services/backup/crypto.js';
 import { registerBackupRoutes } from '../src/routes/backup.js';
-import type { IMcpServerRepository, IMcpProfileRepository } from '../src/repositories/interfaces.js';
+import type { IMcpServerRepository, ISecretRepository } from '../src/repositories/interfaces.js';
 import type { IProjectRepository } from '../src/repositories/project.repository.js';
 
 // Mock data
@@ -12,19 +12,19 @@ const mockServers = [
   {
     id: 's1', name: 'github', description: 'GitHub MCP', packageName: '@mcp/github',
     dockerImage: null, transport: 'STDIO' as const, repositoryUrl: null,
-    envTemplate: [], version: 1, createdAt: new Date(), updatedAt: new Date(),
+    env: [], version: 1, createdAt: new Date(), updatedAt: new Date(),
   },
   {
     id: 's2', name: 'slack', description: 'Slack MCP', packageName: null,
     dockerImage: 'mcp/slack:latest', transport: 'SSE' as const, repositoryUrl: null,
-    envTemplate: [], version: 1, createdAt: new Date(), updatedAt: new Date(),
+    env: [], version: 1, createdAt: new Date(), updatedAt: new Date(),
   },
 ];
 
-const mockProfiles = [
+const mockSecrets = [
   {
-    id: 'p1', name: 'default', serverId: 's1', permissions: ['read'],
-    envOverrides: { GITHUB_TOKEN: 'ghp_secret123' },
+    id: 'sec1', name: 'github-secrets',
+    data: { GITHUB_TOKEN: 'ghp_secret123' },
     version: 1, createdAt: new Date(), updatedAt: new Date(),
   },
 ];
@@ -41,19 +41,19 @@ function mockServerRepo(): IMcpServerRepository {
     findAll: vi.fn(async () => [...mockServers]),
     findById: vi.fn(async (id: string) => mockServers.find((s) => s.id === id) ?? null),
     findByName: vi.fn(async (name: string) => mockServers.find((s) => s.name === name) ?? null),
-    create: vi.fn(async (data) => ({ id: 'new-s', ...data, envTemplate: [], version: 1, createdAt: new Date(), updatedAt: new Date() } as typeof mockServers[0])),
+    create: vi.fn(async (data) => ({ id: 'new-s', ...data, env: [], version: 1, createdAt: new Date(), updatedAt: new Date() } as typeof mockServers[0])),
     update: vi.fn(async (id, data) => ({ ...mockServers.find((s) => s.id === id)!, ...data })),
     delete: vi.fn(async () => {}),
   };
 }
 
-function mockProfileRepo(): IMcpProfileRepository {
+function mockSecretRepo(): ISecretRepository {
   return {
-    findAll: vi.fn(async () => [...mockProfiles]),
-    findById: vi.fn(async (id: string) => mockProfiles.find((p) => p.id === id) ?? null),
-    findByServerAndName: vi.fn(async () => null),
-    create: vi.fn(async (data) => ({ id: 'new-p', ...data, version: 1, createdAt: new Date(), updatedAt: new Date() } as typeof mockProfiles[0])),
-    update: vi.fn(async (id, data) => ({ ...mockProfiles.find((p) => p.id === id)!, ...data })),
+    findAll: vi.fn(async () => [...mockSecrets]),
+    findById: vi.fn(async (id: string) => mockSecrets.find((s) => s.id === id) ?? null),
+    findByName: vi.fn(async (name: string) => mockSecrets.find((s) => s.name === name) ?? null),
+    create: vi.fn(async (data) => ({ id: 'new-sec', ...data, version: 1, createdAt: new Date(), updatedAt: new Date() } as typeof mockSecrets[0])),
+    update: vi.fn(async (id, data) => ({ ...mockSecrets.find((s) => s.id === id)!, ...data })),
     delete: vi.fn(async () => {}),
   };
 }
@@ -66,8 +66,6 @@ function mockProjectRepo(): IProjectRepository {
     create: vi.fn(async (data) => ({ id: 'new-proj', ...data, version: 1, createdAt: new Date(), updatedAt: new Date() } as typeof mockProjects[0])),
     update: vi.fn(async (id, data) => ({ ...mockProjects.find((p) => p.id === id)!, ...data })),
     delete: vi.fn(async () => {}),
-    setProfiles: vi.fn(async () => {}),
-    getProfileIds: vi.fn(async () => ['p1']),
   };
 }
 
@@ -112,7 +110,7 @@ describe('BackupService', () => {
   let backupService: BackupService;
 
   beforeEach(() => {
-    backupService = new BackupService(mockServerRepo(), mockProfileRepo(), mockProjectRepo());
+    backupService = new BackupService(mockServerRepo(), mockProjectRepo(), mockSecretRepo());
   });
 
   it('creates backup with all resources', async () => {
@@ -121,43 +119,43 @@ describe('BackupService', () => {
     expect(bundle.version).toBe('1');
     expect(bundle.encrypted).toBe(false);
     expect(bundle.servers).toHaveLength(2);
-    expect(bundle.profiles).toHaveLength(1);
+    expect(bundle.secrets).toHaveLength(1);
     expect(bundle.projects).toHaveLength(1);
     expect(bundle.servers[0]!.name).toBe('github');
-    expect(bundle.profiles[0]!.serverName).toBe('github');
+    expect(bundle.secrets[0]!.name).toBe('github-secrets');
     expect(bundle.projects[0]!.name).toBe('my-project');
   });
 
   it('filters resources', async () => {
     const bundle = await backupService.createBackup({ resources: ['servers'] });
     expect(bundle.servers).toHaveLength(2);
-    expect(bundle.profiles).toHaveLength(0);
+    expect(bundle.secrets).toHaveLength(0);
     expect(bundle.projects).toHaveLength(0);
   });
 
-  it('encrypts sensitive env values when password provided', async () => {
+  it('encrypts sensitive secret values when password provided', async () => {
     const bundle = await backupService.createBackup({ password: 'test-pass' });
 
     expect(bundle.encrypted).toBe(true);
     expect(bundle.encryptedSecrets).toBeDefined();
     // The GITHUB_TOKEN should be replaced with placeholder
-    const overrides = bundle.profiles[0]!.envOverrides as Record<string, string>;
-    expect(overrides['GITHUB_TOKEN']).toContain('__ENCRYPTED:');
+    const data = bundle.secrets[0]!.data;
+    expect(data['GITHUB_TOKEN']).toContain('__ENCRYPTED:');
   });
 
   it('handles empty repositories', async () => {
     const emptyServerRepo = mockServerRepo();
     (emptyServerRepo.findAll as ReturnType<typeof vi.fn>).mockResolvedValue([]);
-    const emptyProfileRepo = mockProfileRepo();
-    (emptyProfileRepo.findAll as ReturnType<typeof vi.fn>).mockResolvedValue([]);
+    const emptySecretRepo = mockSecretRepo();
+    (emptySecretRepo.findAll as ReturnType<typeof vi.fn>).mockResolvedValue([]);
     const emptyProjectRepo = mockProjectRepo();
     (emptyProjectRepo.findAll as ReturnType<typeof vi.fn>).mockResolvedValue([]);
 
-    const service = new BackupService(emptyServerRepo, emptyProfileRepo, emptyProjectRepo);
+    const service = new BackupService(emptyServerRepo, emptyProjectRepo, emptySecretRepo);
     const bundle = await service.createBackup();
 
     expect(bundle.servers).toHaveLength(0);
-    expect(bundle.profiles).toHaveLength(0);
+    expect(bundle.secrets).toHaveLength(0);
     expect(bundle.projects).toHaveLength(0);
   });
 });
@@ -165,18 +163,18 @@ describe('BackupService', () => {
 describe('RestoreService', () => {
   let restoreService: RestoreService;
   let serverRepo: IMcpServerRepository;
-  let profileRepo: IMcpProfileRepository;
+  let secretRepo: ISecretRepository;
   let projectRepo: IProjectRepository;
 
   beforeEach(() => {
     serverRepo = mockServerRepo();
-    profileRepo = mockProfileRepo();
+    secretRepo = mockSecretRepo();
     projectRepo = mockProjectRepo();
     // Default: nothing exists yet
     (serverRepo.findByName as ReturnType<typeof vi.fn>).mockResolvedValue(null);
-    (profileRepo.findByServerAndName as ReturnType<typeof vi.fn>).mockResolvedValue(null);
+    (secretRepo.findByName as ReturnType<typeof vi.fn>).mockResolvedValue(null);
     (projectRepo.findByName as ReturnType<typeof vi.fn>).mockResolvedValue(null);
-    restoreService = new RestoreService(serverRepo, profileRepo, projectRepo);
+    restoreService = new RestoreService(serverRepo, projectRepo, secretRepo);
   });
 
   const validBundle = {
@@ -184,9 +182,9 @@ describe('RestoreService', () => {
     mcpctlVersion: '0.1.0',
     createdAt: new Date().toISOString(),
     encrypted: false,
-    servers: [{ name: 'github', description: 'GitHub', packageName: null, dockerImage: null, transport: 'STDIO', repositoryUrl: null, envTemplate: [] }],
-    profiles: [{ name: 'default', serverName: 'github', permissions: ['read'], envOverrides: {} }],
-    projects: [{ name: 'test-proj', description: 'Test', profileNames: ['default'] }],
+    servers: [{ name: 'github', description: 'GitHub', packageName: null, dockerImage: null, transport: 'STDIO', repositoryUrl: null, env: [] }],
+    secrets: [{ name: 'github-secrets', data: { GITHUB_TOKEN: 'ghp_123' } }],
+    projects: [{ name: 'test-proj', description: 'Test' }],
   };
 
   it('validates valid bundle', () => {
@@ -203,11 +201,11 @@ describe('RestoreService', () => {
     const result = await restoreService.restore(validBundle);
 
     expect(result.serversCreated).toBe(1);
-    expect(result.profilesCreated).toBe(1);
+    expect(result.secretsCreated).toBe(1);
     expect(result.projectsCreated).toBe(1);
     expect(result.errors).toHaveLength(0);
     expect(serverRepo.create).toHaveBeenCalled();
-    expect(profileRepo.create).toHaveBeenCalled();
+    expect(secretRepo.create).toHaveBeenCalled();
     expect(projectRepo.create).toHaveBeenCalled();
   });
 
@@ -242,17 +240,17 @@ describe('RestoreService', () => {
   });
 
   it('restores encrypted bundle with correct password', async () => {
-    const secrets = { 'profile:default:API_KEY': 'secret-val' };
+    const encryptedData = { 'secret:github-secrets:GITHUB_TOKEN': 'ghp_decrypted' };
     const encBundle = {
       ...validBundle,
       encrypted: true,
-      encryptedSecrets: encrypt(JSON.stringify(secrets), 'test-pw'),
-      profiles: [{ ...validBundle.profiles[0]!, envOverrides: { API_KEY: '__ENCRYPTED:profile:default:API_KEY__' } }],
+      encryptedSecrets: encrypt(JSON.stringify(encryptedData), 'test-pw'),
+      secrets: [{ name: 'github-secrets', data: { GITHUB_TOKEN: '__ENCRYPTED:secret:github-secrets:GITHUB_TOKEN__' } }],
     };
 
     const result = await restoreService.restore(encBundle, { password: 'test-pw' });
     expect(result.errors).toHaveLength(0);
-    expect(result.profilesCreated).toBe(1);
+    expect(result.secretsCreated).toBe(1);
   });
 
   it('fails with wrong decryption password', async () => {
@@ -272,17 +270,17 @@ describe('Backup Routes', () => {
 
   beforeEach(() => {
     const sRepo = mockServerRepo();
-    const pRepo = mockProfileRepo();
+    const secRepo = mockSecretRepo();
     const prRepo = mockProjectRepo();
-    backupService = new BackupService(sRepo, pRepo, prRepo);
+    backupService = new BackupService(sRepo, prRepo, secRepo);
 
     const rSRepo = mockServerRepo();
     (rSRepo.findByName as ReturnType<typeof vi.fn>).mockResolvedValue(null);
-    const rPRepo = mockProfileRepo();
-    (rPRepo.findByServerAndName as ReturnType<typeof vi.fn>).mockResolvedValue(null);
+    const rSecRepo = mockSecretRepo();
+    (rSecRepo.findByName as ReturnType<typeof vi.fn>).mockResolvedValue(null);
     const rPrRepo = mockProjectRepo();
     (rPrRepo.findByName as ReturnType<typeof vi.fn>).mockResolvedValue(null);
-    restoreService = new RestoreService(rSRepo, rPRepo, rPrRepo);
+    restoreService = new RestoreService(rSRepo, rPrRepo, rSecRepo);
   });
 
   async function buildApp() {
@@ -303,7 +301,7 @@ describe('Backup Routes', () => {
     const body = res.json();
     expect(body.version).toBe('1');
     expect(body.servers).toBeDefined();
-    expect(body.profiles).toBeDefined();
+    expect(body.secrets).toBeDefined();
     expect(body.projects).toBeDefined();
   });
 

src/mcpd/tests/env-resolver.test.ts

@@ -0,0 +1,112 @@
+import { describe, it, expect, vi } from 'vitest';
+import { resolveServerEnv } from '../src/services/env-resolver.js';
+import type { ISecretRepository } from '../src/repositories/interfaces.js';
+import type { McpServer } from '@prisma/client';
+
+function makeServer(env: unknown[]): McpServer {
+  return {
+    id: 'srv-1',
+    name: 'test-server',
+    description: '',
+    packageName: null,
+    dockerImage: 'test:latest',
+    transport: 'STDIO',
+    repositoryUrl: null,
+    externalUrl: null,
+    command: null,
+    containerPort: null,
+    replicas: 1,
+    env,
+    version: 1,
+    createdAt: new Date(),
+    updatedAt: new Date(),
+  } as McpServer;
+}
+
+function mockSecretRepo(secrets: Record<string, Record<string, string>>): ISecretRepository {
+  return {
+    findAll: vi.fn(async () => []),
+    findById: vi.fn(async () => null),
+    findByName: vi.fn(async (name: string) => {
+      const data = secrets[name];
+      if (!data) return null;
+      return { id: `sec-${name}`, name, data, version: 1, createdAt: new Date(), updatedAt: new Date() };
+    }),
+    create: vi.fn(async () => ({} as never)),
+    update: vi.fn(async () => ({} as never)),
+    delete: vi.fn(async () => {}),
+  };
+}
+
+describe('resolveServerEnv', () => {
+  it('resolves inline values', async () => {
+    const server = makeServer([
+      { name: 'FOO', value: 'bar' },
+      { name: 'BAZ', value: 'qux' },
+    ]);
+    const repo = mockSecretRepo({});
+    const result = await resolveServerEnv(server, repo);
+    expect(result).toEqual({ FOO: 'bar', BAZ: 'qux' });
+  });
+
+  it('resolves secret references', async () => {
+    const server = makeServer([
+      { name: 'TOKEN', valueFrom: { secretRef: { name: 'ha-creds', key: 'HOMEASSISTANT_TOKEN' } } },
+    ]);
+    const repo = mockSecretRepo({
+      'ha-creds': { HOMEASSISTANT_TOKEN: 'secret-token-123' },
+    });
+    const result = await resolveServerEnv(server, repo);
+    expect(result).toEqual({ TOKEN: 'secret-token-123' });
+  });
+
+  it('handles mixed inline and secret refs', async () => {
+    const server = makeServer([
+      { name: 'URL', value: 'https://ha.local' },
+      { name: 'TOKEN', valueFrom: { secretRef: { name: 'creds', key: 'TOKEN' } } },
+    ]);
+    const repo = mockSecretRepo({
+      creds: { TOKEN: 'my-token' },
+    });
+    const result = await resolveServerEnv(server, repo);
+    expect(result).toEqual({ URL: 'https://ha.local', TOKEN: 'my-token' });
+  });
+
+  it('caches secret lookups', async () => {
+    const server = makeServer([
+      { name: 'A', valueFrom: { secretRef: { name: 'shared', key: 'KEY_A' } } },
+      { name: 'B', valueFrom: { secretRef: { name: 'shared', key: 'KEY_B' } } },
+    ]);
+    const repo = mockSecretRepo({
+      shared: { KEY_A: 'val-a', KEY_B: 'val-b' },
+    });
+    const result = await resolveServerEnv(server, repo);
+    expect(result).toEqual({ A: 'val-a', B: 'val-b' });
+    expect(repo.findByName).toHaveBeenCalledTimes(1);
+  });
+
+  it('throws when secret not found', async () => {
+    const server = makeServer([
+      { name: 'TOKEN', valueFrom: { secretRef: { name: 'missing', key: 'TOKEN' } } },
+    ]);
+    const repo = mockSecretRepo({});
+    await expect(resolveServerEnv(server, repo)).rejects.toThrow("Secret 'missing' not found");
+  });
+
+  it('throws when secret key not found', async () => {
+    const server = makeServer([
+      { name: 'TOKEN', valueFrom: { secretRef: { name: 'creds', key: 'NONEXISTENT' } } },
+    ]);
+    const repo = mockSecretRepo({
+      creds: { OTHER_KEY: 'val' },
+    });
+    await expect(resolveServerEnv(server, repo)).rejects.toThrow("Key 'NONEXISTENT' not found in secret 'creds'");
+  });
+
+  it('returns empty map for empty env', async () => {
+    const server = makeServer([]);
+    const repo = mockSecretRepo({});
+    const result = await resolveServerEnv(server, repo);
+    expect(result).toEqual({});
+  });
+});

src/mcpd/tests/instance-service.test.ts

@@ -3,6 +3,7 @@ import { InstanceService, InvalidStateError } from '../src/services/instance.ser
 import { NotFoundError } from '../src/services/mcp-server.service.js';
 import type { IMcpInstanceRepository, IMcpServerRepository } from '../src/repositories/interfaces.js';
 import type { McpOrchestrator } from '../src/services/orchestrator.js';
+import type { McpInstance } from '@prisma/client';
 
 function mockInstanceRepo(): IMcpInstanceRepository {
   return {
@@ -69,6 +70,41 @@ function mockOrchestrator(): McpOrchestrator {
   };
 }
 
+function makeServer(overrides: Partial<{ id: string; name: string; replicas: number; dockerImage: string | null; externalUrl: string | null; transport: string; command: unknown; containerPort: number | null }> = {}) {
+  return {
+    id: overrides.id ?? 'srv-1',
+    name: overrides.name ?? 'slack',
+    dockerImage: overrides.dockerImage ?? 'ghcr.io/slack-mcp:latest',
+    packageName: null,
+    transport: overrides.transport ?? 'STDIO',
+    description: '',
+    repositoryUrl: null,
+    externalUrl: overrides.externalUrl ?? null,
+    command: overrides.command ?? null,
+    containerPort: overrides.containerPort ?? null,
+    replicas: overrides.replicas ?? 1,
+    env: [],
+    version: 1,
+    createdAt: new Date(),
+    updatedAt: new Date(),
+  };
+}
+
+function makeInstance(overrides: Partial<McpInstance> = {}): McpInstance {
+  return {
+    id: 'inst-1',
+    serverId: 'srv-1',
+    containerId: overrides.containerId ?? 'ctr-abc',
+    status: overrides.status ?? 'RUNNING',
+    port: overrides.port ?? 3000,
+    metadata: overrides.metadata ?? {},
+    version: 1,
+    createdAt: overrides.createdAt ?? new Date(),
+    updatedAt: new Date(),
+    ...overrides,
+  } as McpInstance;
+}
+
 describe('InstanceService', () => {
   let instanceRepo: ReturnType<typeof mockInstanceRepo>;
   let serverRepo: ReturnType<typeof mockServerRepo>;
@@ -101,199 +137,98 @@ describe('InstanceService', () => {
     });
 
     it('returns instance when found', async () => {
-      vi.mocked(instanceRepo.findById).mockResolvedValue({ id: 'inst-1' } as never);
+      vi.mocked(instanceRepo.findById).mockResolvedValue(makeInstance({ id: 'inst-1' }));
       const result = await service.getById('inst-1');
       expect(result.id).toBe('inst-1');
     });
   });
 
-  describe('start', () => {
+  describe('reconcile', () => {
+    it('starts instances when below desired replicas', async () => {
+      vi.mocked(serverRepo.findById).mockResolvedValue(makeServer({ replicas: 2 }));
+      vi.mocked(instanceRepo.findAll).mockResolvedValue([]);
+
+      await service.reconcile('srv-1');
+
+      // Should create 2 instances
+      expect(instanceRepo.create).toHaveBeenCalledTimes(2);
+    });
+
+    it('does nothing when at desired replicas', async () => {
+      vi.mocked(serverRepo.findById).mockResolvedValue(makeServer({ replicas: 1 }));
+      vi.mocked(instanceRepo.findAll).mockResolvedValue([makeInstance({ status: 'RUNNING' })]);
+
+      await service.reconcile('srv-1');
+
+      expect(instanceRepo.create).not.toHaveBeenCalled();
+      expect(instanceRepo.delete).not.toHaveBeenCalled();
+    });
+
+    it('removes excess instances when above desired replicas', async () => {
+      vi.mocked(serverRepo.findById).mockResolvedValue(makeServer({ replicas: 1 }));
+      vi.mocked(instanceRepo.findAll).mockResolvedValue([
+        makeInstance({ id: 'inst-old', createdAt: new Date('2025-01-01') }),
+        makeInstance({ id: 'inst-new', createdAt: new Date('2025-06-01') }),
+      ]);
+
+      await service.reconcile('srv-1');
+
+      // Should remove the oldest one
+      expect(orchestrator.stopContainer).toHaveBeenCalledTimes(1);
+      expect(instanceRepo.delete).toHaveBeenCalledWith('inst-old');
+    });
+
+    it('creates external instances without Docker', async () => {
+      vi.mocked(serverRepo.findById).mockResolvedValue(
+        makeServer({ replicas: 1, externalUrl: 'http://localhost:8086/mcp', dockerImage: null }),
+      );
+      vi.mocked(instanceRepo.findAll).mockResolvedValue([]);
+
+      await service.reconcile('srv-1');
+
+      expect(instanceRepo.create).toHaveBeenCalledWith(
+        expect.objectContaining({ status: 'RUNNING', metadata: expect.objectContaining({ external: true }) }),
+      );
+      expect(orchestrator.createContainer).not.toHaveBeenCalled();
+    });
+
+    it('handles replicas: 0 by removing all instances', async () => {
+      vi.mocked(serverRepo.findById).mockResolvedValue(makeServer({ replicas: 0 }));
+      vi.mocked(instanceRepo.findAll).mockResolvedValue([makeInstance()]);
+
+      await service.reconcile('srv-1');
+
+      expect(instanceRepo.delete).toHaveBeenCalledTimes(1);
+    });
+
     it('throws NotFoundError for unknown server', async () => {
-      await expect(service.start('missing')).rejects.toThrow(NotFoundError);
-    });
-
-    it('creates instance and starts container', async () => {
-      vi.mocked(serverRepo.findById).mockResolvedValue({
-        id: 'srv-1', name: 'slack', dockerImage: 'ghcr.io/slack-mcp:latest',
-        packageName: null, transport: 'STDIO', description: '', repositoryUrl: null,
-        envTemplate: [], version: 1, createdAt: new Date(), updatedAt: new Date(),
-      });
-
-      const result = await service.start('srv-1');
-
-      expect(instanceRepo.create).toHaveBeenCalledWith({
-        serverId: 'srv-1',
-        status: 'STARTING',
-      });
-      expect(orchestrator.createContainer).toHaveBeenCalled();
-      expect(instanceRepo.updateStatus).toHaveBeenCalledWith(
-        'inst-1', 'RUNNING',
-        expect.objectContaining({ containerId: 'ctr-abc123' }),
-      );
-      expect(result.status).toBe('RUNNING');
-    });
-
-    it('marks instance as ERROR on container failure', async () => {
-      vi.mocked(serverRepo.findById).mockResolvedValue({
-        id: 'srv-1', name: 'slack', dockerImage: 'ghcr.io/slack-mcp:latest',
-        packageName: null, transport: 'STDIO', description: '', repositoryUrl: null,
-        envTemplate: [], version: 1, createdAt: new Date(), updatedAt: new Date(),
-      });
-      vi.mocked(orchestrator.createContainer).mockRejectedValue(new Error('Docker unavailable'));
-
-      const result = await service.start('srv-1');
-
-      expect(instanceRepo.updateStatus).toHaveBeenCalledWith(
-        'inst-1', 'ERROR',
-        expect.objectContaining({ metadata: { error: 'Docker unavailable' } }),
-      );
-      expect(result.status).toBe('ERROR');
-    });
-
-    it('uses dockerImage for container spec', async () => {
-      vi.mocked(serverRepo.findById).mockResolvedValue({
-        id: 'srv-1', name: 'slack', dockerImage: 'myregistry.com/slack:v1',
-        packageName: '@slack/mcp', transport: 'SSE', description: '', repositoryUrl: null,
-        envTemplate: [], version: 1, createdAt: new Date(), updatedAt: new Date(),
-      });
-
-      await service.start('srv-1');
-
-      const spec = vi.mocked(orchestrator.createContainer).mock.calls[0]?.[0];
-      expect(spec?.image).toBe('myregistry.com/slack:v1');
-      expect(spec?.containerPort).toBe(3000); // SSE transport
-    });
-  });
-
-  describe('stop', () => {
-    it('throws NotFoundError for missing instance', async () => {
-      await expect(service.stop('missing')).rejects.toThrow(NotFoundError);
-    });
-
-    it('stops a running container', async () => {
-      vi.mocked(instanceRepo.findById).mockResolvedValue({
-        id: 'inst-1', containerId: 'ctr-abc', status: 'RUNNING',
-        serverId: 'srv-1', port: 3000, metadata: {},
-        version: 1, createdAt: new Date(), updatedAt: new Date(),
-      });
-
-      await service.stop('inst-1');
-
-      expect(orchestrator.stopContainer).toHaveBeenCalledWith('ctr-abc');
-      expect(instanceRepo.updateStatus).toHaveBeenCalledWith('inst-1', 'STOPPED');
-    });
-
-    it('handles stop without containerId', async () => {
-      vi.mocked(instanceRepo.findById).mockResolvedValue({
-        id: 'inst-1', containerId: null, status: 'ERROR',
-        serverId: 'srv-1', port: null, metadata: {},
-        version: 1, createdAt: new Date(), updatedAt: new Date(),
-      });
-
-      await service.stop('inst-1');
-
-      expect(orchestrator.stopContainer).not.toHaveBeenCalled();
-      expect(instanceRepo.updateStatus).toHaveBeenCalledWith('inst-1', 'STOPPED');
-    });
-
-    it('throws InvalidStateError when already stopped', async () => {
-      vi.mocked(instanceRepo.findById).mockResolvedValue({
-        id: 'inst-1', containerId: 'ctr-abc', status: 'STOPPED',
-        serverId: 'srv-1', port: null, metadata: {},
-        version: 1, createdAt: new Date(), updatedAt: new Date(),
-      });
-
-      await expect(service.stop('inst-1')).rejects.toThrow(InvalidStateError);
-    });
-  });
-
-  describe('restart', () => {
-    it('stops, removes, and starts a new instance', async () => {
-      vi.mocked(instanceRepo.findById).mockResolvedValue({
-        id: 'inst-1', containerId: 'ctr-abc', status: 'RUNNING',
-        serverId: 'srv-1', port: 3000, metadata: {},
-        version: 1, createdAt: new Date(), updatedAt: new Date(),
-      });
-      vi.mocked(serverRepo.findById).mockResolvedValue({
-        id: 'srv-1', name: 'slack', dockerImage: 'slack:latest',
-        packageName: null, transport: 'STDIO', description: '', repositoryUrl: null,
-        envTemplate: [], version: 1, createdAt: new Date(), updatedAt: new Date(),
-      });
-
-      const result = await service.restart('inst-1');
-
-      expect(orchestrator.stopContainer).toHaveBeenCalledWith('ctr-abc');
-      expect(orchestrator.removeContainer).toHaveBeenCalledWith('ctr-abc', true);
-      expect(instanceRepo.delete).toHaveBeenCalledWith('inst-1');
-      expect(instanceRepo.create).toHaveBeenCalled();
-      expect(result.status).toBe('RUNNING');
-    });
-
-    it('handles restart when container already stopped', async () => {
-      vi.mocked(instanceRepo.findById).mockResolvedValue({
-        id: 'inst-1', containerId: 'ctr-abc', status: 'STOPPED',
-        serverId: 'srv-1', port: null, metadata: {},
-        version: 1, createdAt: new Date(), updatedAt: new Date(),
-      });
-      vi.mocked(serverRepo.findById).mockResolvedValue({
-        id: 'srv-1', name: 'slack', dockerImage: 'slack:latest',
-        packageName: null, transport: 'STDIO', description: '', repositoryUrl: null,
-        envTemplate: [], version: 1, createdAt: new Date(), updatedAt: new Date(),
-      });
-
-      const result = await service.restart('inst-1');
-
-      // Should not try to stop an already-stopped container
-      expect(orchestrator.stopContainer).not.toHaveBeenCalled();
-      expect(instanceRepo.delete).toHaveBeenCalledWith('inst-1');
-      expect(result.status).toBe('RUNNING');
-    });
-  });
-
-  describe('inspect', () => {
-    it('returns container info', async () => {
-      vi.mocked(instanceRepo.findById).mockResolvedValue({
-        id: 'inst-1', containerId: 'ctr-abc', status: 'RUNNING',
-        serverId: 'srv-1', port: 3000, metadata: {},
-        version: 1, createdAt: new Date(), updatedAt: new Date(),
-      });
-
-      const result = await service.inspect('inst-1');
-      expect(orchestrator.inspectContainer).toHaveBeenCalledWith('ctr-abc');
-      expect(result.containerId).toBe('ctr-abc123');
-    });
-
-    it('throws InvalidStateError when no container', async () => {
-      vi.mocked(instanceRepo.findById).mockResolvedValue({
-        id: 'inst-1', containerId: null, status: 'ERROR',
-        serverId: 'srv-1', port: null, metadata: {},
-        version: 1, createdAt: new Date(), updatedAt: new Date(),
-      });
-
-      await expect(service.inspect('inst-1')).rejects.toThrow(InvalidStateError);
+      await expect(service.reconcile('missing')).rejects.toThrow(NotFoundError);
     });
   });
 
   describe('remove', () => {
-    it('removes container and DB record', async () => {
-      vi.mocked(instanceRepo.findById).mockResolvedValue({
-        id: 'inst-1', containerId: 'ctr-abc', status: 'STOPPED',
-        serverId: 'srv-1', port: null, metadata: {},
-        version: 1, createdAt: new Date(), updatedAt: new Date(),
-      });
+    it('stops container and deletes DB record', async () => {
+      vi.mocked(instanceRepo.findById).mockResolvedValue(makeInstance({ containerId: 'ctr-abc' }));
+
+      const result = await service.remove('inst-1');
+
+      expect(orchestrator.stopContainer).toHaveBeenCalledWith('ctr-abc');
+      expect(orchestrator.removeContainer).toHaveBeenCalledWith('ctr-abc', true);
+      expect(instanceRepo.delete).toHaveBeenCalledWith('inst-1');
+      expect(result.serverId).toBe('srv-1');
+    });
+
+    it('deletes DB record for external instance (no container)', async () => {
+      vi.mocked(instanceRepo.findById).mockResolvedValue(makeInstance({ containerId: null }));
 
       await service.remove('inst-1');
 
-      expect(orchestrator.removeContainer).toHaveBeenCalledWith('ctr-abc', true);
+      expect(orchestrator.stopContainer).not.toHaveBeenCalled();
       expect(instanceRepo.delete).toHaveBeenCalledWith('inst-1');
     });
 
-    it('removes DB record even if container is already gone', async () => {
-      vi.mocked(instanceRepo.findById).mockResolvedValue({
-        id: 'inst-1', containerId: 'ctr-abc', status: 'STOPPED',
-        serverId: 'srv-1', port: null, metadata: {},
-        version: 1, createdAt: new Date(), updatedAt: new Date(),
-      });
+    it('deletes DB record even if container is already gone', async () => {
+      vi.mocked(instanceRepo.findById).mockResolvedValue(makeInstance({ containerId: 'ctr-abc' }));
       vi.mocked(orchestrator.removeContainer).mockRejectedValue(new Error('No such container'));
 
       await service.remove('inst-1');
@@ -302,24 +237,56 @@ describe('InstanceService', () => {
     });
   });
 
+  describe('removeAllForServer', () => {
+    it('stops all containers for a server', async () => {
+      vi.mocked(instanceRepo.findAll).mockResolvedValue([
+        makeInstance({ id: 'inst-1', containerId: 'ctr-1' }),
+        makeInstance({ id: 'inst-2', containerId: 'ctr-2' }),
+      ]);
+
+      await service.removeAllForServer('srv-1');
+
+      expect(orchestrator.stopContainer).toHaveBeenCalledTimes(2);
+      expect(orchestrator.removeContainer).toHaveBeenCalledTimes(2);
+    });
+
+    it('skips external instances with no container', async () => {
+      vi.mocked(instanceRepo.findAll).mockResolvedValue([
+        makeInstance({ id: 'inst-1', containerId: null }),
+      ]);
+
+      await service.removeAllForServer('srv-1');
+
+      expect(orchestrator.stopContainer).not.toHaveBeenCalled();
+    });
+  });
+
+  describe('inspect', () => {
+    it('returns container info', async () => {
+      vi.mocked(instanceRepo.findById).mockResolvedValue(makeInstance({ containerId: 'ctr-abc' }));
+
+      const result = await service.inspect('inst-1');
+      expect(orchestrator.inspectContainer).toHaveBeenCalledWith('ctr-abc');
+      expect(result.containerId).toBe('ctr-abc123');
+    });
+
+    it('throws InvalidStateError when no container', async () => {
+      vi.mocked(instanceRepo.findById).mockResolvedValue(makeInstance({ containerId: null }));
+
+      await expect(service.inspect('inst-1')).rejects.toThrow(InvalidStateError);
+    });
+  });
+
   describe('getLogs', () => {
     it('returns empty logs for instance without container', async () => {
-      vi.mocked(instanceRepo.findById).mockResolvedValue({
-        id: 'inst-1', containerId: null, status: 'ERROR',
-        serverId: 'srv-1', port: null, metadata: {},
-        version: 1, createdAt: new Date(), updatedAt: new Date(),
-      });
+      vi.mocked(instanceRepo.findById).mockResolvedValue(makeInstance({ containerId: null }));
 
       const result = await service.getLogs('inst-1');
       expect(result).toEqual({ stdout: '', stderr: '' });
     });
 
     it('returns container logs', async () => {
-      vi.mocked(instanceRepo.findById).mockResolvedValue({
-        id: 'inst-1', containerId: 'ctr-abc', status: 'RUNNING',
-        serverId: 'srv-1', port: 3000, metadata: {},
-        version: 1, createdAt: new Date(), updatedAt: new Date(),
-      });
+      vi.mocked(instanceRepo.findById).mockResolvedValue(makeInstance({ containerId: 'ctr-abc' }));
 
       const result = await service.getLogs('inst-1', { tail: 50 });
 

src/mcpd/tests/mcp-config-generator.test.ts

@@ -1,22 +1,8 @@
 import { describe, it, expect } from 'vitest';
 import { generateMcpConfig } from '../src/services/mcp-config-generator.js';
-import type { ProfileWithServer } from '../src/services/mcp-config-generator.js';
+import type { McpServer } from '@prisma/client';
 
-function makeProfile(overrides: Partial<ProfileWithServer['profile']> = {}): ProfileWithServer['profile'] {
-  return {
-    id: 'p1',
-    name: 'default',
-    serverId: 's1',
-    permissions: [],
-    envOverrides: {},
-    version: 1,
-    createdAt: new Date(),
-    updatedAt: new Date(),
-    ...overrides,
-  };
-}
-
-function makeServer(overrides: Partial<ProfileWithServer['server']> = {}): ProfileWithServer['server'] {
+function makeServer(overrides: Partial<McpServer> = {}): McpServer {
   return {
     id: 's1',
     name: 'slack',
@@ -25,7 +11,7 @@ function makeServer(overrides: Partial<ProfileWithServer['server']> = {}): Profi
     dockerImage: null,
     transport: 'STDIO',
     repositoryUrl: null,
-    envTemplate: [],
+    env: [],
     version: 1,
     createdAt: new Date(),
     updatedAt: new Date(),
@@ -34,76 +20,51 @@ function makeServer(overrides: Partial<ProfileWithServer['server']> = {}): Profi
 }
 
 describe('generateMcpConfig', () => {
-  it('returns empty mcpServers for empty profiles', () => {
+  it('returns empty mcpServers for empty input', () => {
     const result = generateMcpConfig([]);
     expect(result).toEqual({ mcpServers: {} });
   });
 
-  it('generates config for a single profile', () => {
+  it('generates config for a single server', () => {
     const result = generateMcpConfig([
-      { profile: makeProfile(), server: makeServer() },
+      { server: makeServer(), resolvedEnv: {} },
     ]);
-    expect(result.mcpServers['slack--default']).toBeDefined();
-    expect(result.mcpServers['slack--default']?.command).toBe('npx');
-    expect(result.mcpServers['slack--default']?.args).toEqual(['-y', '@anthropic/slack-mcp']);
+    expect(result.mcpServers['slack']).toBeDefined();
+    expect(result.mcpServers['slack']?.command).toBe('npx');
+    expect(result.mcpServers['slack']?.args).toEqual(['-y', '@anthropic/slack-mcp']);
   });
 
-  it('excludes secret env vars from output', () => {
-    const server = makeServer({
-      envTemplate: [
-        { name: 'SLACK_BOT_TOKEN', description: 'Token', isSecret: true },
-        { name: 'SLACK_TEAM_ID', description: 'Team', isSecret: false, defaultValue: 'T123' },
-      ] as never,
-    });
+  it('includes resolved env when present', () => {
     const result = generateMcpConfig([
-      { profile: makeProfile(), server },
+      { server: makeServer(), resolvedEnv: { SLACK_TEAM_ID: 'T123' } },
     ]);
-    const config = result.mcpServers['slack--default'];
+    const config = result.mcpServers['slack'];
     expect(config?.env).toBeDefined();
     expect(config?.env?.['SLACK_TEAM_ID']).toBe('T123');
-    expect(config?.env?.['SLACK_BOT_TOKEN']).toBeUndefined();
   });
 
-  it('applies env overrides from profile (non-secret only)', () => {
-    const server = makeServer({
-      envTemplate: [
-        { name: 'API_URL', description: 'URL', isSecret: false },
-      ] as never,
-    });
-    const profile = makeProfile({
-      envOverrides: { API_URL: 'https://staging.example.com' } as never,
-    });
-    const result = generateMcpConfig([{ profile, server }]);
-    expect(result.mcpServers['slack--default']?.env?.['API_URL']).toBe('https://staging.example.com');
+  it('omits env when resolvedEnv is empty', () => {
+    const result = generateMcpConfig([
+      { server: makeServer(), resolvedEnv: {} },
+    ]);
+    expect(result.mcpServers['slack']?.env).toBeUndefined();
   });
 
   it('generates multiple server configs', () => {
     const result = generateMcpConfig([
-      { profile: makeProfile({ name: 'readonly' }), server: makeServer({ name: 'slack' }) },
-      { profile: makeProfile({ name: 'default', id: 'p2' }), server: makeServer({ name: 'github', id: 's2', packageName: '@anthropic/github-mcp' }) },
+      { server: makeServer({ name: 'slack' }), resolvedEnv: {} },
+      { server: makeServer({ name: 'github', id: 's2', packageName: '@anthropic/github-mcp' }), resolvedEnv: {} },
     ]);
     expect(Object.keys(result.mcpServers)).toHaveLength(2);
-    expect(result.mcpServers['slack--readonly']).toBeDefined();
-    expect(result.mcpServers['github--default']).toBeDefined();
-  });
-
-  it('omits env when no non-secret vars have values', () => {
-    const server = makeServer({
-      envTemplate: [
-        { name: 'TOKEN', description: 'Secret', isSecret: true },
-      ] as never,
-    });
-    const result = generateMcpConfig([
-      { profile: makeProfile(), server },
-    ]);
-    expect(result.mcpServers['slack--default']?.env).toBeUndefined();
+    expect(result.mcpServers['slack']).toBeDefined();
+    expect(result.mcpServers['github']).toBeDefined();
   });
 
   it('uses server name as fallback when packageName is null', () => {
     const server = makeServer({ packageName: null });
     const result = generateMcpConfig([
-      { profile: makeProfile(), server },
+      { server, resolvedEnv: {} },
     ]);
-    expect(result.mcpServers['slack--default']?.args).toEqual(['-y', 'slack']);
+    expect(result.mcpServers['slack']?.args).toEqual(['-y', 'slack']);
   });
 });

src/mcpd/tests/mcp-profile-service.test.ts

@@ -1,128 +0,0 @@
-import { describe, it, expect, vi, beforeEach } from 'vitest';
-import { McpProfileService } from '../src/services/mcp-profile.service.js';
-import { NotFoundError, ConflictError } from '../src/services/mcp-server.service.js';
-import type { IMcpProfileRepository, IMcpServerRepository } from '../src/repositories/interfaces.js';
-
-function mockProfileRepo(): IMcpProfileRepository {
-  return {
-    findAll: vi.fn(async () => []),
-    findById: vi.fn(async () => null),
-    findByServerAndName: vi.fn(async () => null),
-    create: vi.fn(async (data) => ({
-      id: 'new-id',
-      name: data.name,
-      serverId: data.serverId,
-      permissions: data.permissions ?? [],
-      envOverrides: data.envOverrides ?? {},
-      version: 1,
-      createdAt: new Date(),
-      updatedAt: new Date(),
-    })),
-    update: vi.fn(async (id, data) => ({
-      id,
-      name: data.name ?? 'test',
-      serverId: 'srv-1',
-      permissions: data.permissions ?? [],
-      envOverrides: data.envOverrides ?? {},
-      version: 2,
-      createdAt: new Date(),
-      updatedAt: new Date(),
-    })),
-    delete: vi.fn(async () => {}),
-  };
-}
-
-function mockServerRepo(): IMcpServerRepository {
-  return {
-    findAll: vi.fn(async () => []),
-    findById: vi.fn(async () => null),
-    findByName: vi.fn(async () => null),
-    create: vi.fn(async () => ({} as never)),
-    update: vi.fn(async () => ({} as never)),
-    delete: vi.fn(async () => {}),
-  };
-}
-
-describe('McpProfileService', () => {
-  let profileRepo: ReturnType<typeof mockProfileRepo>;
-  let serverRepo: ReturnType<typeof mockServerRepo>;
-  let service: McpProfileService;
-
-  beforeEach(() => {
-    profileRepo = mockProfileRepo();
-    serverRepo = mockServerRepo();
-    service = new McpProfileService(profileRepo, serverRepo);
-  });
-
-  describe('list', () => {
-    it('returns all profiles', async () => {
-      await service.list();
-      expect(profileRepo.findAll).toHaveBeenCalledWith(undefined);
-    });
-
-    it('filters by serverId', async () => {
-      await service.list('srv-1');
-      expect(profileRepo.findAll).toHaveBeenCalledWith('srv-1');
-    });
-  });
-
-  describe('getById', () => {
-    it('returns profile when found', async () => {
-      vi.mocked(profileRepo.findById).mockResolvedValue({ id: '1', name: 'test' } as never);
-      const result = await service.getById('1');
-      expect(result.id).toBe('1');
-    });
-
-    it('throws NotFoundError when not found', async () => {
-      await expect(service.getById('missing')).rejects.toThrow(NotFoundError);
-    });
-  });
-
-  describe('create', () => {
-    it('creates a profile when server exists', async () => {
-      vi.mocked(serverRepo.findById).mockResolvedValue({ id: 'srv-1', name: 'test' } as never);
-      const result = await service.create({ name: 'readonly', serverId: 'srv-1' });
-      expect(result.name).toBe('readonly');
-    });
-
-    it('throws NotFoundError when server does not exist', async () => {
-      await expect(service.create({ name: 'test', serverId: 'missing' })).rejects.toThrow(NotFoundError);
-    });
-
-    it('throws ConflictError when profile name exists for server', async () => {
-      vi.mocked(serverRepo.findById).mockResolvedValue({ id: 'srv-1', name: 'test' } as never);
-      vi.mocked(profileRepo.findByServerAndName).mockResolvedValue({ id: '1' } as never);
-      await expect(service.create({ name: 'dup', serverId: 'srv-1' })).rejects.toThrow(ConflictError);
-    });
-  });
-
-  describe('update', () => {
-    it('updates an existing profile', async () => {
-      vi.mocked(profileRepo.findById).mockResolvedValue({ id: '1', name: 'old', serverId: 'srv-1' } as never);
-      await service.update('1', { permissions: ['read'] });
-      expect(profileRepo.update).toHaveBeenCalled();
-    });
-
-    it('checks uniqueness when renaming', async () => {
-      vi.mocked(profileRepo.findById).mockResolvedValue({ id: '1', name: 'old', serverId: 'srv-1' } as never);
-      vi.mocked(profileRepo.findByServerAndName).mockResolvedValue({ id: '2' } as never);
-      await expect(service.update('1', { name: 'taken' })).rejects.toThrow(ConflictError);
-    });
-
-    it('throws NotFoundError when profile does not exist', async () => {
-      await expect(service.update('missing', {})).rejects.toThrow(NotFoundError);
-    });
-  });
-
-  describe('delete', () => {
-    it('deletes an existing profile', async () => {
-      vi.mocked(profileRepo.findById).mockResolvedValue({ id: '1' } as never);
-      await service.delete('1');
-      expect(profileRepo.delete).toHaveBeenCalledWith('1');
-    });
-
-    it('throws NotFoundError when profile does not exist', async () => {
-      await expect(service.delete('missing')).rejects.toThrow(NotFoundError);
-    });
-  });
-});

src/mcpd/tests/mcp-server-flow.test.ts

@@ -0,0 +1,727 @@
+import { describe, it, expect, vi, beforeAll, afterAll, beforeEach } from 'vitest';
+import Fastify from 'fastify';
+import type { FastifyInstance } from 'fastify';
+import http from 'node:http';
+import { McpServerService } from '../src/services/mcp-server.service.js';
+import { InstanceService } from '../src/services/instance.service.js';
+import { McpProxyService } from '../src/services/mcp-proxy-service.js';
+import { AuditLogService } from '../src/services/audit-log.service.js';
+import { errorHandler } from '../src/middleware/error-handler.js';
+import { registerMcpServerRoutes } from '../src/routes/mcp-servers.js';
+import { registerInstanceRoutes } from '../src/routes/instances.js';
+import { registerMcpProxyRoutes } from '../src/routes/mcp-proxy.js';
+import type {
+  IMcpServerRepository,
+  IMcpInstanceRepository,
+  IAuditLogRepository,
+} from '../src/repositories/interfaces.js';
+import type { McpOrchestrator } from '../src/services/orchestrator.js';
+import type { McpServer, McpInstance, InstanceStatus } from '@prisma/client';
+
+// ---------------------------------------------------------------------------
+// In-memory repository implementations (stateful mocks)
+// ---------------------------------------------------------------------------
+
+function createInMemoryServerRepo(): IMcpServerRepository {
+  const servers = new Map<string, McpServer>();
+  let nextId = 1;
+
+  return {
+    findAll: vi.fn(async () => [...servers.values()]),
+    findById: vi.fn(async (id: string) => servers.get(id) ?? null),
+    findByName: vi.fn(async (name: string) => [...servers.values()].find((s) => s.name === name) ?? null),
+    create: vi.fn(async (data) => {
+      const id = `srv-${nextId++}`;
+      const server = {
+        id,
+        name: data.name,
+        description: data.description ?? '',
+        packageName: data.packageName ?? null,
+        dockerImage: data.dockerImage ?? null,
+        transport: data.transport ?? 'STDIO',
+        repositoryUrl: data.repositoryUrl ?? null,
+        externalUrl: data.externalUrl ?? null,
+        command: data.command ?? null,
+        containerPort: data.containerPort ?? null,
+        replicas: data.replicas ?? 1,
+        env: data.env ?? [],
+        version: 1,
+        createdAt: new Date(),
+        updatedAt: new Date(),
+      } as McpServer;
+      servers.set(id, server);
+      return server;
+    }),
+    update: vi.fn(async (id: string, data) => {
+      const existing = servers.get(id);
+      if (!existing) throw new Error(`Server ${id} not found`);
+      const updated = { ...existing, ...data, updatedAt: new Date() } as McpServer;
+      servers.set(id, updated);
+      return updated;
+    }),
+    delete: vi.fn(async (id: string) => {
+      servers.delete(id);
+    }),
+  };
+}
+
+function createInMemoryInstanceRepo(): IMcpInstanceRepository {
+  const instances = new Map<string, McpInstance>();
+  let nextId = 1;
+
+  return {
+    findAll: vi.fn(async (serverId?: string) => {
+      const all = [...instances.values()];
+      return serverId ? all.filter((i) => i.serverId === serverId) : all;
+    }),
+    findById: vi.fn(async (id: string) => instances.get(id) ?? null),
+    findByContainerId: vi.fn(async (containerId: string) =>
+      [...instances.values()].find((i) => i.containerId === containerId) ?? null,
+    ),
+    create: vi.fn(async (data) => {
+      const id = `inst-${nextId++}`;
+      const instance = {
+        id,
+        serverId: data.serverId,
+        containerId: data.containerId ?? null,
+        status: (data.status ?? 'STOPPED') as InstanceStatus,
+        port: data.port ?? null,
+        metadata: data.metadata ?? {},
+        version: 1,
+        createdAt: new Date(),
+        updatedAt: new Date(),
+      } as McpInstance;
+      instances.set(id, instance);
+      return instance;
+    }),
+    updateStatus: vi.fn(async (id: string, status: InstanceStatus, fields?) => {
+      const existing = instances.get(id);
+      if (!existing) throw new Error(`Instance ${id} not found`);
+      const updated = {
+        ...existing,
+        status,
+        ...(fields?.containerId !== undefined ? { containerId: fields.containerId } : {}),
+        ...(fields?.port !== undefined ? { port: fields.port } : {}),
+        ...(fields?.metadata !== undefined ? { metadata: fields.metadata } : {}),
+        version: existing.version + 1,
+        updatedAt: new Date(),
+      } as McpInstance;
+      instances.set(id, updated);
+      return updated;
+    }),
+    delete: vi.fn(async (id: string) => {
+      instances.delete(id);
+    }),
+  };
+}
+
+function createInMemoryAuditLogRepo(): IAuditLogRepository {
+  const logs: Array<{ id: string; userId: string; action: string; resource: string; resourceId: string | null; details: Record<string, unknown>; createdAt: Date }> = [];
+  let nextId = 1;
+
+  return {
+    findAll: vi.fn(async () => logs as never[]),
+    findById: vi.fn(async (id: string) => (logs.find((l) => l.id === id) as never) ?? null),
+    create: vi.fn(async (data) => {
+      const log = {
+        id: `log-${nextId++}`,
+        userId: data.userId,
+        action: data.action,
+        resource: data.resource,
+        resourceId: data.resourceId ?? null,
+        details: data.details ?? {},
+        createdAt: new Date(),
+      };
+      logs.push(log);
+      return log as never;
+    }),
+    count: vi.fn(async () => logs.length),
+    deleteOlderThan: vi.fn(async () => 0),
+  };
+}
+
+function createMockOrchestrator(): McpOrchestrator {
+  let containerPort = 40000;
+  return {
+    ping: vi.fn(async () => true),
+    pullImage: vi.fn(async () => {}),
+    createContainer: vi.fn(async (spec) => ({
+      containerId: `ctr-${spec.name}`,
+      name: spec.name,
+      state: 'running' as const,
+      port: spec.containerPort ?? ++containerPort,
+      createdAt: new Date(),
+    })),
+    stopContainer: vi.fn(async () => {}),
+    removeContainer: vi.fn(async () => {}),
+    inspectContainer: vi.fn(async (id) => ({
+      containerId: id,
+      name: 'test',
+      state: 'running' as const,
+      createdAt: new Date(),
+    })),
+    getContainerLogs: vi.fn(async () => ({ stdout: '', stderr: '' })),
+  };
+}
+
+// ---------------------------------------------------------------------------
+// Fake MCP server (streamable-http)
+// ---------------------------------------------------------------------------
+
+function createFakeMcpServer(): { server: http.Server; getPort: () => number; requests: Array<{ method: string; body: unknown }> } {
+  const requests: Array<{ method: string; body: unknown }> = [];
+  let sessionCounter = 0;
+
+  const server = http.createServer((req, res) => {
+    let body = '';
+    req.on('data', (chunk) => (body += chunk));
+    req.on('end', () => {
+      let parsed: { method?: string; id?: number; params?: unknown } = {};
+      try {
+        parsed = JSON.parse(body);
+      } catch {
+        // notifications may not have id
+      }
+
+      requests.push({ method: parsed.method ?? 'unknown', body: parsed });
+
+      if (parsed.method === 'initialize') {
+        const sessionId = `session-${++sessionCounter}`;
+        const response = {
+          jsonrpc: '2.0',
+          id: parsed.id,
+          result: {
+            protocolVersion: '2025-03-26',
+            capabilities: { tools: {} },
+            serverInfo: { name: 'fake-mcp', version: '1.0.0' },
+          },
+        };
+        res.writeHead(200, {
+          'Content-Type': 'text/event-stream',
+          'Mcp-Session-Id': sessionId,
+        });
+        res.end(`event: message\ndata: ${JSON.stringify(response)}\n\n`);
+        return;
+      }
+
+      if (parsed.method === 'notifications/initialized') {
+        res.writeHead(200, { 'Content-Type': 'application/json' });
+        res.end('');
+        return;
+      }
+
+      if (parsed.method === 'tools/list') {
+        const response = {
+          jsonrpc: '2.0',
+          id: parsed.id,
+          result: {
+            tools: [
+              { name: 'ha_get_overview', description: 'Get Home Assistant overview', inputSchema: { type: 'object', properties: {} } },
+              { name: 'ha_search_entities', description: 'Search HA entities', inputSchema: { type: 'object', properties: { query: { type: 'string' } } } },
+            ],
+          },
+        };
+        res.writeHead(200, { 'Content-Type': 'text/event-stream' });
+        res.end(`event: message\ndata: ${JSON.stringify(response)}\n\n`);
+        return;
+      }
+
+      if (parsed.method === 'tools/call') {
+        const toolName = (parsed.params as { name?: string })?.name;
+        const response = {
+          jsonrpc: '2.0',
+          id: parsed.id,
+          result: {
+            content: [{ type: 'text', text: `Result from ${toolName}` }],
+          },
+        };
+        res.writeHead(200, { 'Content-Type': 'text/event-stream' });
+        res.end(`event: message\ndata: ${JSON.stringify(response)}\n\n`);
+        return;
+      }
+
+      // Default: echo back
+      res.writeHead(200, { 'Content-Type': 'application/json' });
+      res.end(JSON.stringify({ jsonrpc: '2.0', id: parsed.id, result: {} }));
+    });
+  });
+
+  let port = 0;
+  return {
+    server,
+    getPort: () => port,
+    requests,
+    ...{
+      listen: () =>
+        new Promise<void>((resolve) => {
+          server.listen(0, () => {
+            const addr = server.address();
+            if (addr && typeof addr === 'object') port = addr.port;
+            resolve();
+          });
+        }),
+      close: () => new Promise<void>((resolve) => server.close(() => resolve())),
+    },
+  } as ReturnType<typeof createFakeMcpServer> & { listen: () => Promise<void>; close: () => Promise<void> };
+}
+
+// ---------------------------------------------------------------------------
+// Test app builder
+// ---------------------------------------------------------------------------
+
+async function buildTestApp(deps: {
+  serverRepo: IMcpServerRepository;
+  instanceRepo: IMcpInstanceRepository;
+  auditLogRepo: IAuditLogRepository;
+  orchestrator: McpOrchestrator;
+}): Promise<FastifyInstance> {
+  const app = Fastify({ logger: false });
+  app.setErrorHandler(errorHandler);
+
+  const serverService = new McpServerService(deps.serverRepo);
+  const instanceService = new InstanceService(deps.instanceRepo, deps.serverRepo, deps.orchestrator);
+  serverService.setInstanceService(instanceService);
+  const proxyService = new McpProxyService(deps.instanceRepo, deps.serverRepo);
+  const auditLogService = new AuditLogService(deps.auditLogRepo);
+
+  registerMcpServerRoutes(app, serverService, instanceService);
+  registerInstanceRoutes(app, instanceService);
+  registerMcpProxyRoutes(app, {
+    mcpProxyService: proxyService,
+    auditLogService,
+    authDeps: {
+      findSession: async () => ({ userId: 'test-user', expiresAt: new Date(Date.now() + 3600_000) }),
+    },
+  });
+
+  await app.ready();
+  return app;
+}
+
+// ---------------------------------------------------------------------------
+// Tests
+// ---------------------------------------------------------------------------
+
+describe('MCP server full flow', () => {
+  let fakeMcp: ReturnType<typeof createFakeMcpServer> & { listen: () => Promise<void>; close: () => Promise<void> };
+  let fakeMcpPort: number;
+
+  beforeAll(async () => {
+    fakeMcp = createFakeMcpServer() as typeof fakeMcp;
+    await fakeMcp.listen();
+    fakeMcpPort = fakeMcp.getPort();
+  });
+
+  afterAll(async () => {
+    await fakeMcp.close();
+  });
+
+  describe('external server flow (externalUrl)', () => {
+    let app: FastifyInstance;
+    let serverRepo: IMcpServerRepository;
+    let instanceRepo: IMcpInstanceRepository;
+
+    beforeEach(async () => {
+      serverRepo = createInMemoryServerRepo();
+      instanceRepo = createInMemoryInstanceRepo();
+      app = await buildTestApp({
+        serverRepo,
+        instanceRepo,
+        auditLogRepo: createInMemoryAuditLogRepo(),
+        orchestrator: createMockOrchestrator(),
+      });
+    });
+
+    afterAll(async () => {
+      if (app) await app.close();
+    });
+
+    it('registers server (auto-creates instance via reconcile), and proxies tools/list', async () => {
+      // 1. Register external MCP server (replicas defaults to 1 → auto-creates instance)
+      const createRes = await app.inject({
+        method: 'POST',
+        url: '/api/v1/servers',
+        payload: {
+          name: 'ha-mcp',
+          description: 'Home Assistant MCP',
+          transport: 'STREAMABLE_HTTP',
+          externalUrl: `http://localhost:${fakeMcpPort}`,
+          containerPort: 3000,
+          env: [
+            { name: 'HOMEASSISTANT_TOKEN', value: 'placeholder' },
+          ],
+        },
+      });
+
+      expect(createRes.statusCode).toBe(201);
+      const server = createRes.json<{ id: string; name: string; externalUrl: string }>();
+      expect(server.name).toBe('ha-mcp');
+      expect(server.externalUrl).toBe(`http://localhost:${fakeMcpPort}`);
+
+      // 2. Verify server is listed
+      const listRes = await app.inject({ method: 'GET', url: '/api/v1/servers' });
+      expect(listRes.statusCode).toBe(200);
+      const servers = listRes.json<Array<{ name: string }>>();
+      expect(servers).toHaveLength(1);
+      expect(servers[0]!.name).toBe('ha-mcp');
+
+      // 3. Verify instance was auto-created (no Docker for external servers)
+      const instancesRes = await app.inject({
+        method: 'GET',
+        url: `/api/v1/instances?serverId=${server.id}`,
+      });
+      expect(instancesRes.statusCode).toBe(200);
+      const instances = instancesRes.json<Array<{ id: string; status: string; containerId: string | null }>>();
+      expect(instances).toHaveLength(1);
+      expect(instances[0]!.status).toBe('RUNNING');
+      expect(instances[0]!.containerId).toBeNull();
+
+      // 4. Proxy tools/list to the fake MCP server
+      const proxyRes = await app.inject({
+        method: 'POST',
+        url: '/api/v1/mcp/proxy',
+        headers: { authorization: 'Bearer test-token' },
+        payload: {
+          serverId: server.id,
+          method: 'tools/list',
+        },
+      });
+
+      expect(proxyRes.statusCode).toBe(200);
+      const proxyBody = proxyRes.json<{ jsonrpc: string; result: { tools: Array<{ name: string }> } }>();
+      expect(proxyBody.jsonrpc).toBe('2.0');
+      expect(proxyBody.result.tools).toHaveLength(2);
+      expect(proxyBody.result.tools.map((t) => t.name)).toContain('ha_get_overview');
+      expect(proxyBody.result.tools.map((t) => t.name)).toContain('ha_search_entities');
+
+      // 5. Verify the fake server received the protocol handshake + tools/list
+      const methods = fakeMcp.requests.map((r) => r.method);
+      expect(methods).toContain('initialize');
+      expect(methods).toContain('notifications/initialized');
+      expect(methods).toContain('tools/list');
+    });
+
+    it('proxies tools/call with parameters', async () => {
+      // Register (auto-creates instance via reconcile)
+      const createRes = await app.inject({
+        method: 'POST',
+        url: '/api/v1/servers',
+        payload: {
+          name: 'ha-mcp-call',
+          description: 'HA MCP for call test',
+          transport: 'STREAMABLE_HTTP',
+          externalUrl: `http://localhost:${fakeMcpPort}`,
+        },
+      });
+      const server = createRes.json<{ id: string }>();
+
+      // Proxy tools/call (instance was auto-created)
+      const proxyRes = await app.inject({
+        method: 'POST',
+        url: '/api/v1/mcp/proxy',
+        headers: { authorization: 'Bearer test-token' },
+        payload: {
+          serverId: server.id,
+          method: 'tools/call',
+          params: { name: 'ha_get_overview' },
+        },
+      });
+
+      expect(proxyRes.statusCode).toBe(200);
+      const body = proxyRes.json<{ result: { content: Array<{ text: string }> } }>();
+      expect(body.result.content[0]!.text).toBe('Result from ha_get_overview');
+    });
+  });
+
+  describe('managed server flow (Docker)', () => {
+    let app: FastifyInstance;
+    let orchestrator: ReturnType<typeof createMockOrchestrator>;
+
+    beforeEach(async () => {
+      orchestrator = createMockOrchestrator();
+      app = await buildTestApp({
+        serverRepo: createInMemoryServerRepo(),
+        instanceRepo: createInMemoryInstanceRepo(),
+        auditLogRepo: createInMemoryAuditLogRepo(),
+        orchestrator,
+      });
+    });
+
+    afterAll(async () => {
+      if (app) await app.close();
+    });
+
+    it('registers server with dockerImage, auto-creates container instance via reconcile', async () => {
+      // 1. Register managed server (replicas: 1 → auto-creates container)
+      const createRes = await app.inject({
+        method: 'POST',
+        url: '/api/v1/servers',
+        payload: {
+          name: 'ha-mcp-docker',
+          description: 'HA MCP managed by Docker',
+          dockerImage: 'ghcr.io/homeassistant-ai/ha-mcp:2.4',
+          transport: 'STREAMABLE_HTTP',
+          containerPort: 3000,
+          command: ['python', '-c', 'print("hello")'],
+          env: [
+            { name: 'HOMEASSISTANT_URL', value: 'http://localhost:8123' },
+            { name: 'HOMEASSISTANT_TOKEN', valueFrom: { secretRef: { name: 'ha-secrets', key: 'token' } } },
+          ],
+        },
+      });
+
+      expect(createRes.statusCode).toBe(201);
+      const server = createRes.json<{ id: string; name: string; dockerImage: string; command: string[] }>();
+      expect(server.name).toBe('ha-mcp-docker');
+      expect(server.dockerImage).toBe('ghcr.io/homeassistant-ai/ha-mcp:2.4');
+      expect(server.command).toEqual(['python', '-c', 'print("hello")']);
+
+      // 2. Verify instance was auto-created with container
+      const instancesRes = await app.inject({
+        method: 'GET',
+        url: `/api/v1/instances?serverId=${server.id}`,
+      });
+      expect(instancesRes.statusCode).toBe(200);
+      const instances = instancesRes.json<Array<{ id: string; status: string; containerId: string }>>();
+      expect(instances).toHaveLength(1);
+      expect(instances[0]!.status).toBe('RUNNING');
+      expect(instances[0]!.containerId).toBeTruthy();
+
+      // 3. Verify orchestrator was called with correct spec
+      expect(orchestrator.createContainer).toHaveBeenCalledTimes(1);
+      const spec = vi.mocked(orchestrator.createContainer).mock.calls[0]![0];
+      expect(spec.image).toBe('ghcr.io/homeassistant-ai/ha-mcp:2.4');
+      expect(spec.containerPort).toBe(3000);
+      expect(spec.command).toEqual(['python', '-c', 'print("hello")']);
+    });
+
+    it('marks instance as ERROR when Docker fails', async () => {
+      vi.mocked(orchestrator.createContainer).mockRejectedValueOnce(new Error('Docker socket unavailable'));
+
+      // Creating server triggers reconcile which tries to create container → fails
+      const createRes = await app.inject({
+        method: 'POST',
+        url: '/api/v1/servers',
+        payload: {
+          name: 'failing-server',
+          description: 'Will fail to start',
+          dockerImage: 'some-image:latest',
+          transport: 'STDIO',
+        },
+      });
+      expect(createRes.statusCode).toBe(201);
+
+      const server = createRes.json<{ id: string }>();
+      const instancesRes = await app.inject({
+        method: 'GET',
+        url: `/api/v1/instances?serverId=${server.id}`,
+      });
+      const instances = instancesRes.json<Array<{ id: string; status: string }>>();
+      expect(instances).toHaveLength(1);
+      expect(instances[0]!.status).toBe('ERROR');
+    });
+  });
+
+  describe('full lifecycle', () => {
+    let app: FastifyInstance;
+    let orchestrator: ReturnType<typeof createMockOrchestrator>;
+
+    beforeEach(async () => {
+      orchestrator = createMockOrchestrator();
+      app = await buildTestApp({
+        serverRepo: createInMemoryServerRepo(),
+        instanceRepo: createInMemoryInstanceRepo(),
+        auditLogRepo: createInMemoryAuditLogRepo(),
+        orchestrator,
+      });
+    });
+
+    afterAll(async () => {
+      if (app) await app.close();
+    });
+
+    it('register → auto-create → list → delete instance (reconcile) → delete server (cascade)', async () => {
+      // Register (auto-creates instance via reconcile)
+      const createRes = await app.inject({
+        method: 'POST',
+        url: '/api/v1/servers',
+        payload: {
+          name: 'lifecycle-test',
+          description: 'Full lifecycle',
+          dockerImage: 'test:latest',
+          transport: 'SSE',
+          containerPort: 8080,
+        },
+      });
+      expect(createRes.statusCode).toBe(201);
+      const server = createRes.json<{ id: string }>();
+
+      // List instances (auto-created)
+      const listRes = await app.inject({
+        method: 'GET',
+        url: `/api/v1/instances?serverId=${server.id}`,
+      });
+      expect(listRes.statusCode).toBe(200);
+      const instances = listRes.json<Array<{ id: string; status: string }>>();
+      expect(instances).toHaveLength(1);
+      expect(instances[0]!.status).toBe('RUNNING');
+      const instanceId = instances[0]!.id;
+
+      // Delete instance → triggers reconcile → new instance auto-created
+      const removeRes = await app.inject({
+        method: 'DELETE',
+        url: `/api/v1/instances/${instanceId}`,
+      });
+      expect(removeRes.statusCode).toBe(204);
+
+      // Verify a replacement instance was created (reconcile)
+      const listAfter = await app.inject({
+        method: 'GET',
+        url: `/api/v1/instances?serverId=${server.id}`,
+      });
+      const afterInstances = listAfter.json<Array<{ id: string }>>();
+      expect(afterInstances).toHaveLength(1);
+      expect(afterInstances[0]!.id).not.toBe(instanceId); // New instance, not the old one
+
+      // Delete server (cascade removes all instances)
+      const deleteRes = await app.inject({
+        method: 'DELETE',
+        url: `/api/v1/servers/${server.id}`,
+      });
+      expect(deleteRes.statusCode).toBe(204);
+
+      // Verify server is gone
+      const serversAfter = await app.inject({ method: 'GET', url: '/api/v1/servers' });
+      expect(serversAfter.json<unknown[]>()).toHaveLength(0);
+    });
+
+    it('external server lifecycle: register → auto-create → proxy → delete server (cascade)', async () => {
+      // Register external (auto-creates virtual instance)
+      const createRes = await app.inject({
+        method: 'POST',
+        url: '/api/v1/servers',
+        payload: {
+          name: 'external-lifecycle',
+          transport: 'STREAMABLE_HTTP',
+          externalUrl: `http://localhost:${fakeMcpPort}`,
+        },
+      });
+      const server = createRes.json<{ id: string }>();
+
+      // Verify auto-created instance
+      const instancesRes = await app.inject({
+        method: 'GET',
+        url: `/api/v1/instances?serverId=${server.id}`,
+      });
+      const instances = instancesRes.json<Array<{ id: string; status: string; containerId: string | null }>>();
+      expect(instances).toHaveLength(1);
+      expect(instances[0]!.status).toBe('RUNNING');
+      expect(instances[0]!.containerId).toBeNull();
+
+      // Proxy tools/list
+      const proxyRes = await app.inject({
+        method: 'POST',
+        url: '/api/v1/mcp/proxy',
+        headers: { authorization: 'Bearer test-token' },
+        payload: { serverId: server.id, method: 'tools/list' },
+      });
+      expect(proxyRes.statusCode).toBe(200);
+      expect(proxyRes.json<{ result: { tools: unknown[] } }>().result.tools.length).toBeGreaterThan(0);
+
+      // Docker orchestrator should NOT have been called (external server)
+      expect(orchestrator.createContainer).not.toHaveBeenCalled();
+      expect(orchestrator.stopContainer).not.toHaveBeenCalled();
+
+      // Delete server (cascade)
+      const deleteRes = await app.inject({
+        method: 'DELETE',
+        url: `/api/v1/servers/${server.id}`,
+      });
+      expect(deleteRes.statusCode).toBe(204);
+    });
+  });
+
+  describe('proxy authentication', () => {
+    let app: FastifyInstance;
+
+    beforeEach(async () => {
+      app = await buildTestApp({
+        serverRepo: createInMemoryServerRepo(),
+        instanceRepo: createInMemoryInstanceRepo(),
+        auditLogRepo: createInMemoryAuditLogRepo(),
+        orchestrator: createMockOrchestrator(),
+      });
+    });
+
+    afterAll(async () => {
+      if (app) await app.close();
+    });
+
+    it('rejects proxy calls without auth header', async () => {
+      const res = await app.inject({
+        method: 'POST',
+        url: '/api/v1/mcp/proxy',
+        payload: { serverId: 'srv-1', method: 'tools/list' },
+      });
+      // Auth middleware rejects with 401 (no Bearer token)
+      expect(res.statusCode).toBe(401);
+    });
+  });
+
+  describe('server update flow', () => {
+    let app: FastifyInstance;
+
+    beforeEach(async () => {
+      app = await buildTestApp({
+        serverRepo: createInMemoryServerRepo(),
+        instanceRepo: createInMemoryInstanceRepo(),
+        auditLogRepo: createInMemoryAuditLogRepo(),
+        orchestrator: createMockOrchestrator(),
+      });
+    });
+
+    afterAll(async () => {
+      if (app) await app.close();
+    });
+
+    it('creates and updates server fields', async () => {
+      // Create (with replicas: 0 to avoid creating instances in this test)
+      const createRes = await app.inject({
+        method: 'POST',
+        url: '/api/v1/servers',
+        payload: {
+          name: 'updatable',
+          description: 'Original desc',
+          transport: 'STDIO',
+          replicas: 0,
+        },
+      });
+      expect(createRes.statusCode).toBe(201);
+      const server = createRes.json<{ id: string; description: string }>();
+      expect(server.description).toBe('Original desc');
+
+      // Update
+      const updateRes = await app.inject({
+        method: 'PUT',
+        url: `/api/v1/servers/${server.id}`,
+        payload: {
+          description: 'Updated desc',
+          externalUrl: `http://localhost:${fakeMcpPort}`,
+          transport: 'STREAMABLE_HTTP',
+        },
+      });
+      expect(updateRes.statusCode).toBe(200);
+      const updated = updateRes.json<{ description: string; externalUrl: string; transport: string }>();
+      expect(updated.description).toBe('Updated desc');
+      expect(updated.externalUrl).toBe(`http://localhost:${fakeMcpPort}`);
+      expect(updated.transport).toBe('STREAMABLE_HTTP');
+
+      // Fetch to verify persistence
+      const getRes = await app.inject({
+        method: 'GET',
+        url: `/api/v1/servers/${server.id}`,
+      });
+      expect(getRes.json<{ description: string }>().description).toBe('Updated desc');
+    });
+  });
+});

src/mcpd/tests/mcp-server-routes.test.ts

@@ -3,44 +3,66 @@ import Fastify from 'fastify';
 import type { FastifyInstance } from 'fastify';
 import { registerMcpServerRoutes } from '../src/routes/mcp-servers.js';
 import { McpServerService, NotFoundError, ConflictError } from '../src/services/mcp-server.service.js';
+import { InstanceService } from '../src/services/instance.service.js';
 import { errorHandler } from '../src/middleware/error-handler.js';
-import type { IMcpServerRepository } from '../src/repositories/interfaces.js';
+import type { IMcpServerRepository, IMcpInstanceRepository } from '../src/repositories/interfaces.js';
+import type { McpOrchestrator } from '../src/services/orchestrator.js';
 
 let app: FastifyInstance;
 
 function mockRepo(): IMcpServerRepository {
+  let lastCreated: Record<string, unknown> | null = null;
   return {
     findAll: vi.fn(async () => [
-      { id: '1', name: 'slack', description: 'Slack server', transport: 'STDIO' },
+      { id: '1', name: 'slack', description: 'Slack server', transport: 'STDIO', replicas: 1 },
     ]),
-    findById: vi.fn(async () => null),
+    findById: vi.fn(async (id: string) => {
+      if (lastCreated && (lastCreated as { id: string }).id === id) return lastCreated as never;
+      return null;
+    }),
     findByName: vi.fn(async () => null),
-    create: vi.fn(async (data) => ({
-      id: 'new-id',
-      name: data.name,
-      description: data.description ?? '',
-      packageName: data.packageName ?? null,
-      dockerImage: null,
-      transport: data.transport ?? 'STDIO',
-      repositoryUrl: null,
-      envTemplate: [],
-      version: 1,
-      createdAt: new Date(),
-      updatedAt: new Date(),
-    })),
-    update: vi.fn(async (id, data) => ({
-      id,
-      name: 'slack',
-      description: (data.description as string) ?? 'Slack server',
-      packageName: null,
-      dockerImage: null,
-      transport: 'STDIO',
-      repositoryUrl: null,
-      envTemplate: [],
-      version: 2,
-      createdAt: new Date(),
-      updatedAt: new Date(),
-    })),
+    create: vi.fn(async (data) => {
+      const server = {
+        id: 'new-id',
+        name: data.name,
+        description: data.description ?? '',
+        packageName: data.packageName ?? null,
+        dockerImage: null,
+        transport: data.transport ?? 'STDIO',
+        repositoryUrl: null,
+        externalUrl: null,
+        command: null,
+        containerPort: null,
+        replicas: data.replicas ?? 1,
+        env: [],
+        version: 1,
+        createdAt: new Date(),
+        updatedAt: new Date(),
+      };
+      lastCreated = server;
+      return server;
+    }),
+    update: vi.fn(async (id, data) => {
+      const server = {
+        id,
+        name: 'slack',
+        description: (data.description as string) ?? 'Slack server',
+        packageName: null,
+        dockerImage: null,
+        transport: 'STDIO',
+        repositoryUrl: null,
+        externalUrl: null,
+        command: null,
+        containerPort: null,
+        replicas: 1,
+        env: [],
+        version: 2,
+        createdAt: new Date(),
+        updatedAt: new Date(),
+      };
+      lastCreated = server;
+      return server;
+    }),
     delete: vi.fn(async () => {}),
   };
 }
@@ -49,11 +71,56 @@ afterEach(async () => {
   if (app) await app.close();
 });
 
+function stubInstanceRepo(): IMcpInstanceRepository {
+  return {
+    findAll: vi.fn(async () => []),
+    findById: vi.fn(async () => null),
+    findByContainerId: vi.fn(async () => null),
+    create: vi.fn(async (data) => ({
+      id: 'inst-stub',
+      serverId: data.serverId,
+      containerId: null,
+      status: data.status ?? 'STOPPED',
+      port: null,
+      metadata: {},
+      version: 1,
+      createdAt: new Date(),
+      updatedAt: new Date(),
+    })),
+    updateStatus: vi.fn(async (id, status) => ({
+      id,
+      serverId: 'srv-1',
+      containerId: null,
+      status,
+      port: null,
+      metadata: {},
+      version: 2,
+      createdAt: new Date(),
+      updatedAt: new Date(),
+    })),
+    delete: vi.fn(async () => {}),
+  };
+}
+
+function stubOrchestrator(): McpOrchestrator {
+  return {
+    ping: vi.fn(async () => true),
+    pullImage: vi.fn(async () => {}),
+    createContainer: vi.fn(async () => ({ containerId: 'ctr-stub', name: 'stub', state: 'running' as const, port: 3000, createdAt: new Date() })),
+    stopContainer: vi.fn(async () => {}),
+    removeContainer: vi.fn(async () => {}),
+    inspectContainer: vi.fn(async () => ({ containerId: 'ctr-stub', name: 'stub', state: 'running' as const, createdAt: new Date() })),
+    getContainerLogs: vi.fn(async () => ({ stdout: '', stderr: '' })),
+  };
+}
+
 function createApp(repo: IMcpServerRepository) {
   app = Fastify({ logger: false });
   app.setErrorHandler(errorHandler);
   const service = new McpServerService(repo);
-  registerMcpServerRoutes(app, service);
+  const instanceService = new InstanceService(stubInstanceRepo(), repo, stubOrchestrator());
+  service.setInstanceService(instanceService);
+  registerMcpServerRoutes(app, service, instanceService);
   return app.ready();
 }
 

src/mcpd/tests/mcp-server-service.test.ts

@@ -15,7 +15,7 @@ function mockRepo(): IMcpServerRepository {
       dockerImage: null,
       transport: data.transport ?? 'STDIO',
       repositoryUrl: data.repositoryUrl ?? null,
-      envTemplate: data.envTemplate ?? [],
+      env: data.env ?? [],
       version: 1,
       createdAt: new Date(),
       updatedAt: new Date(),
@@ -28,7 +28,7 @@ function mockRepo(): IMcpServerRepository {
       dockerImage: null,
       transport: 'STDIO' as const,
       repositoryUrl: null,
-      envTemplate: [],
+      env: [],
       version: 2,
       createdAt: new Date(),
       updatedAt: new Date(),

src/mcpd/tests/project-service.test.ts

@@ -2,7 +2,7 @@ import { describe, it, expect, vi, beforeEach } from 'vitest';
 import { ProjectService } from '../src/services/project.service.js';
 import { NotFoundError, ConflictError } from '../src/services/mcp-server.service.js';
 import type { IProjectRepository } from '../src/repositories/project.repository.js';
-import type { IMcpProfileRepository, IMcpServerRepository } from '../src/repositories/interfaces.js';
+import type { IMcpServerRepository } from '../src/repositories/interfaces.js';
 
 function mockProjectRepo(): IProjectRepository {
   return {
@@ -23,19 +23,6 @@ function mockProjectRepo(): IProjectRepository {
       createdAt: new Date(), updatedAt: new Date(),
     })),
     delete: vi.fn(async () => {}),
-    setProfiles: vi.fn(async () => {}),
-    getProfileIds: vi.fn(async () => []),
-  };
-}
-
-function mockProfileRepo(): IMcpProfileRepository {
-  return {
-    findAll: vi.fn(async () => []),
-    findById: vi.fn(async () => null),
-    findByServerAndName: vi.fn(async () => null),
-    create: vi.fn(async () => ({} as never)),
-    update: vi.fn(async () => ({} as never)),
-    delete: vi.fn(async () => {}),
   };
 }
 
@@ -52,15 +39,13 @@ function mockServerRepo(): IMcpServerRepository {
 
 describe('ProjectService', () => {
   let projectRepo: ReturnType<typeof mockProjectRepo>;
-  let profileRepo: ReturnType<typeof mockProfileRepo>;
   let serverRepo: ReturnType<typeof mockServerRepo>;
   let service: ProjectService;
 
   beforeEach(() => {
     projectRepo = mockProjectRepo();
-    profileRepo = mockProfileRepo();
     serverRepo = mockServerRepo();
-    service = new ProjectService(projectRepo, profileRepo, serverRepo);
+    service = new ProjectService(projectRepo, serverRepo);
   });
 
   describe('create', () => {
@@ -86,55 +71,6 @@ describe('ProjectService', () => {
     });
   });
 
-  describe('setProfiles', () => {
-    it('sets profile associations', async () => {
-      vi.mocked(projectRepo.findById).mockResolvedValue({ id: 'p1' } as never);
-      vi.mocked(profileRepo.findById).mockResolvedValue({ id: 'prof-1' } as never);
-      const result = await service.setProfiles('p1', { profileIds: ['prof-1'] });
-      expect(result).toEqual(['prof-1']);
-      expect(projectRepo.setProfiles).toHaveBeenCalledWith('p1', ['prof-1']);
-    });
-
-    it('throws NotFoundError for missing profile', async () => {
-      vi.mocked(projectRepo.findById).mockResolvedValue({ id: 'p1' } as never);
-      await expect(service.setProfiles('p1', { profileIds: ['missing'] })).rejects.toThrow(NotFoundError);
-    });
-
-    it('throws NotFoundError for missing project', async () => {
-      await expect(service.setProfiles('missing', { profileIds: [] })).rejects.toThrow(NotFoundError);
-    });
-  });
-
-  describe('getMcpConfig', () => {
-    it('returns empty config for project with no profiles', async () => {
-      vi.mocked(projectRepo.findById).mockResolvedValue({ id: 'p1' } as never);
-      const result = await service.getMcpConfig('p1');
-      expect(result).toEqual({ mcpServers: {} });
-    });
-
-    it('generates config from profiles', async () => {
-      vi.mocked(projectRepo.findById).mockResolvedValue({ id: 'p1' } as never);
-      vi.mocked(projectRepo.getProfileIds).mockResolvedValue(['prof-1']);
-      vi.mocked(profileRepo.findById).mockResolvedValue({
-        id: 'prof-1', name: 'default', serverId: 's1',
-        permissions: [], envOverrides: {},
-        version: 1, createdAt: new Date(), updatedAt: new Date(),
-      });
-      vi.mocked(serverRepo.findById).mockResolvedValue({
-        id: 's1', name: 'slack', description: '', packageName: '@anthropic/slack-mcp',
-        dockerImage: null, transport: 'STDIO', repositoryUrl: null, envTemplate: [],
-        version: 1, createdAt: new Date(), updatedAt: new Date(),
-      });
-
-      const result = await service.getMcpConfig('p1');
-      expect(result.mcpServers['slack--default']).toBeDefined();
-    });
-
-    it('throws NotFoundError for missing project', async () => {
-      await expect(service.getMcpConfig('missing')).rejects.toThrow(NotFoundError);
-    });
-  });
-
   describe('delete', () => {
     it('deletes project', async () => {
       vi.mocked(projectRepo.findById).mockResolvedValue({ id: 'p1' } as never);

src/mcpd/tests/secret-routes.test.ts

@@ -0,0 +1,170 @@
+import { describe, it, expect, vi, afterEach } from 'vitest';
+import Fastify from 'fastify';
+import type { FastifyInstance } from 'fastify';
+import { registerSecretRoutes } from '../src/routes/secrets.js';
+import { SecretService } from '../src/services/secret.service.js';
+import { errorHandler } from '../src/middleware/error-handler.js';
+import type { ISecretRepository } from '../src/repositories/interfaces.js';
+
+let app: FastifyInstance;
+
+function mockRepo(): ISecretRepository {
+  let lastCreated: Record<string, unknown> | null = null;
+  return {
+    findAll: vi.fn(async () => [
+      { id: '1', name: 'ha-creds', data: { TOKEN: 'abc' }, version: 1, createdAt: new Date(), updatedAt: new Date() },
+    ]),
+    findById: vi.fn(async (id: string) => {
+      if (lastCreated && (lastCreated as { id: string }).id === id) return lastCreated as never;
+      return null;
+    }),
+    findByName: vi.fn(async () => null),
+    create: vi.fn(async (data) => {
+      const secret = {
+        id: 'new-id',
+        name: data.name,
+        data: data.data ?? {},
+        version: 1,
+        createdAt: new Date(),
+        updatedAt: new Date(),
+      };
+      lastCreated = secret;
+      return secret;
+    }),
+    update: vi.fn(async (id, data) => {
+      const secret = {
+        id,
+        name: 'ha-creds',
+        data: data.data,
+        version: 2,
+        createdAt: new Date(),
+        updatedAt: new Date(),
+      };
+      lastCreated = secret;
+      return secret;
+    }),
+    delete: vi.fn(async () => {}),
+  };
+}
+
+afterEach(async () => {
+  if (app) await app.close();
+});
+
+function createApp(repo: ISecretRepository) {
+  app = Fastify({ logger: false });
+  app.setErrorHandler(errorHandler);
+  const service = new SecretService(repo);
+  registerSecretRoutes(app, service);
+  return app.ready();
+}
+
+describe('Secret Routes', () => {
+  describe('GET /api/v1/secrets', () => {
+    it('returns secret list', async () => {
+      const repo = mockRepo();
+      await createApp(repo);
+      const res = await app.inject({ method: 'GET', url: '/api/v1/secrets' });
+      expect(res.statusCode).toBe(200);
+      const body = res.json<Array<{ name: string }>>();
+      expect(body).toHaveLength(1);
+      expect(body[0]?.name).toBe('ha-creds');
+    });
+  });
+
+  describe('GET /api/v1/secrets/:id', () => {
+    it('returns 404 when not found', async () => {
+      const repo = mockRepo();
+      await createApp(repo);
+      const res = await app.inject({ method: 'GET', url: '/api/v1/secrets/missing' });
+      expect(res.statusCode).toBe(404);
+    });
+
+    it('returns secret when found', async () => {
+      const repo = mockRepo();
+      vi.mocked(repo.findById).mockResolvedValue({ id: '1', name: 'ha-creds', data: { TOKEN: 'abc' } } as never);
+      await createApp(repo);
+      const res = await app.inject({ method: 'GET', url: '/api/v1/secrets/1' });
+      expect(res.statusCode).toBe(200);
+    });
+  });
+
+  describe('POST /api/v1/secrets', () => {
+    it('creates a secret and returns 201', async () => {
+      const repo = mockRepo();
+      await createApp(repo);
+      const res = await app.inject({
+        method: 'POST',
+        url: '/api/v1/secrets',
+        payload: { name: 'new-secret', data: { KEY: 'val' } },
+      });
+      expect(res.statusCode).toBe(201);
+      expect(res.json<{ name: string }>().name).toBe('new-secret');
+    });
+
+    it('returns 400 for invalid input', async () => {
+      const repo = mockRepo();
+      await createApp(repo);
+      const res = await app.inject({
+        method: 'POST',
+        url: '/api/v1/secrets',
+        payload: { name: '' },
+      });
+      expect(res.statusCode).toBe(400);
+    });
+
+    it('returns 409 when name already exists', async () => {
+      const repo = mockRepo();
+      vi.mocked(repo.findByName).mockResolvedValue({ id: '1' } as never);
+      await createApp(repo);
+      const res = await app.inject({
+        method: 'POST',
+        url: '/api/v1/secrets',
+        payload: { name: 'existing' },
+      });
+      expect(res.statusCode).toBe(409);
+    });
+  });
+
+  describe('PUT /api/v1/secrets/:id', () => {
+    it('updates a secret', async () => {
+      const repo = mockRepo();
+      vi.mocked(repo.findById).mockResolvedValue({ id: '1', name: 'ha-creds' } as never);
+      await createApp(repo);
+      const res = await app.inject({
+        method: 'PUT',
+        url: '/api/v1/secrets/1',
+        payload: { data: { TOKEN: 'new-val' } },
+      });
+      expect(res.statusCode).toBe(200);
+    });
+
+    it('returns 404 when not found', async () => {
+      const repo = mockRepo();
+      await createApp(repo);
+      const res = await app.inject({
+        method: 'PUT',
+        url: '/api/v1/secrets/missing',
+        payload: { data: { X: 'y' } },
+      });
+      expect(res.statusCode).toBe(404);
+    });
+  });
+
+  describe('DELETE /api/v1/secrets/:id', () => {
+    it('deletes a secret and returns 204', async () => {
+      const repo = mockRepo();
+      vi.mocked(repo.findById).mockResolvedValue({ id: '1', name: 'ha-creds' } as never);
+      await createApp(repo);
+      const res = await app.inject({ method: 'DELETE', url: '/api/v1/secrets/1' });
+      expect(res.statusCode).toBe(204);
+    });
+
+    it('returns 404 when not found', async () => {
+      const repo = mockRepo();
+      await createApp(repo);
+      const res = await app.inject({ method: 'DELETE', url: '/api/v1/secrets/missing' });
+      expect(res.statusCode).toBe(404);
+    });
+  });
+});

src/mcpd/tests/validation.test.ts

@@ -2,8 +2,6 @@ import { describe, it, expect } from 'vitest';
 import {
   CreateMcpServerSchema,
   UpdateMcpServerSchema,
-  CreateMcpProfileSchema,
-  UpdateMcpProfileSchema,
 } from '../src/validation/index.js';
 
 describe('CreateMcpServerSchema', () => {
@@ -14,7 +12,7 @@ describe('CreateMcpServerSchema', () => {
       transport: 'STDIO',
     });
     expect(result.name).toBe('my-server');
-    expect(result.envTemplate).toEqual([]);
+    expect(result.env).toEqual([]);
   });
 
   it('rejects empty name', () => {
@@ -39,15 +37,40 @@ describe('CreateMcpServerSchema', () => {
     expect(result.transport).toBe('STDIO');
   });
 
-  it('validates envTemplate entries', () => {
+  it('validates env entries with inline value', () => {
     const result = CreateMcpServerSchema.parse({
       name: 'test',
-      envTemplate: [
-        { name: 'API_KEY', description: 'The key', isSecret: true },
+      env: [
+        { name: 'API_URL', value: 'https://example.com' },
       ],
     });
-    expect(result.envTemplate).toHaveLength(1);
-    expect(result.envTemplate[0]?.isSecret).toBe(true);
+    expect(result.env).toHaveLength(1);
+    expect(result.env[0]?.value).toBe('https://example.com');
+  });
+
+  it('validates env entries with secretRef', () => {
+    const result = CreateMcpServerSchema.parse({
+      name: 'test',
+      env: [
+        { name: 'API_KEY', valueFrom: { secretRef: { name: 'my-secret', key: 'api-key' } } },
+      ],
+    });
+    expect(result.env).toHaveLength(1);
+    expect(result.env[0]?.valueFrom?.secretRef.name).toBe('my-secret');
+  });
+
+  it('rejects env entry with neither value nor valueFrom', () => {
+    expect(() => CreateMcpServerSchema.parse({
+      name: 'test',
+      env: [{ name: 'FOO' }],
+    })).toThrow();
+  });
+
+  it('rejects env entry with both value and valueFrom', () => {
+    expect(() => CreateMcpServerSchema.parse({
+      name: 'test',
+      env: [{ name: 'FOO', value: 'bar', valueFrom: { secretRef: { name: 'x', key: 'y' } } }],
+    })).toThrow();
   });
 
   it('rejects invalid transport', () => {
@@ -78,47 +101,3 @@ describe('UpdateMcpServerSchema', () => {
   });
 });
 
-describe('CreateMcpProfileSchema', () => {
-  it('validates valid input', () => {
-    const result = CreateMcpProfileSchema.parse({
-      name: 'readonly',
-      serverId: 'server-123',
-    });
-    expect(result.name).toBe('readonly');
-    expect(result.permissions).toEqual([]);
-    expect(result.envOverrides).toEqual({});
-  });
-
-  it('rejects empty name', () => {
-    expect(() => CreateMcpProfileSchema.parse({ name: '', serverId: 'x' })).toThrow();
-  });
-
-  it('accepts permissions array', () => {
-    const result = CreateMcpProfileSchema.parse({
-      name: 'admin',
-      serverId: 'x',
-      permissions: ['read', 'write', 'delete'],
-    });
-    expect(result.permissions).toHaveLength(3);
-  });
-
-  it('accepts envOverrides', () => {
-    const result = CreateMcpProfileSchema.parse({
-      name: 'staging',
-      serverId: 'x',
-      envOverrides: { API_URL: 'https://staging.example.com' },
-    });
-    expect(result.envOverrides['API_URL']).toBe('https://staging.example.com');
-  });
-});
-
-describe('UpdateMcpProfileSchema', () => {
-  it('allows partial updates', () => {
-    const result = UpdateMcpProfileSchema.parse({ permissions: ['read'] });
-    expect(result.permissions).toEqual(['read']);
-  });
-
-  it('allows empty object', () => {
-    expect(UpdateMcpProfileSchema.parse({})).toBeDefined();
-  });
-});

src/shared/src/index.ts

@@ -2,4 +2,3 @@ export * from './types/index.js';
 export * from './validation/index.js';
 export * from './constants/index.js';
 export * from './utils/index.js';
-export * from './profiles/index.js';

src/shared/src/profiles/index.ts

@@ -1,5 +0,0 @@
-export type { ProfileTemplate, ProfileCategory, InstantiatedProfile } from './types.js';
-export { profileTemplateSchema, envTemplateEntrySchema } from './types.js';
-export { ProfileRegistry, defaultRegistry } from './registry.js';
-export { validateTemplate, getMissingEnvVars, instantiateProfile, generateMcpJsonEntry } from './utils.js';
-export * from './templates/index.js';

src/shared/src/profiles/registry.ts

@@ -1,67 +0,0 @@
-import type { ProfileTemplate, ProfileCategory } from './types.js';
-import { filesystemTemplate } from './templates/filesystem.js';
-import { githubTemplate } from './templates/github.js';
-import { postgresTemplate } from './templates/postgres.js';
-import { slackTemplate } from './templates/slack.js';
-import { memoryTemplate } from './templates/memory.js';
-import { fetchTemplate } from './templates/fetch.js';
-
-const builtinTemplates: ProfileTemplate[] = [
-  filesystemTemplate,
-  githubTemplate,
-  postgresTemplate,
-  slackTemplate,
-  memoryTemplate,
-  fetchTemplate,
-];
-
-export class ProfileRegistry {
-  private templates = new Map<string, ProfileTemplate>();
-
-  constructor(templates: ProfileTemplate[] = builtinTemplates) {
-    for (const t of templates) {
-      this.templates.set(t.id, t);
-    }
-  }
-
-  getAll(): ProfileTemplate[] {
-    return [...this.templates.values()];
-  }
-
-  getById(id: string): ProfileTemplate | undefined {
-    return this.templates.get(id);
-  }
-
-  getByCategory(category: ProfileCategory): ProfileTemplate[] {
-    return this.getAll().filter((t) => t.category === category);
-  }
-
-  getCategories(): ProfileCategory[] {
-    const cats = new Set<ProfileCategory>();
-    for (const t of this.templates.values()) {
-      cats.add(t.category);
-    }
-    return [...cats];
-  }
-
-  search(query: string): ProfileTemplate[] {
-    const q = query.toLowerCase();
-    return this.getAll().filter(
-      (t) =>
-        t.id.includes(q) ||
-        t.name.includes(q) ||
-        t.displayName.toLowerCase().includes(q) ||
-        t.description.toLowerCase().includes(q),
-    );
-  }
-
-  register(template: ProfileTemplate): void {
-    this.templates.set(template.id, template);
-  }
-
-  has(id: string): boolean {
-    return this.templates.has(id);
-  }
-}
-
-export const defaultRegistry = new ProfileRegistry();

src/shared/src/profiles/templates/fetch.ts

@@ -1,15 +0,0 @@
-import type { ProfileTemplate } from '../types.js';
-
-export const fetchTemplate: ProfileTemplate = {
-  id: 'fetch',
-  name: 'fetch',
-  displayName: 'Fetch',
-  description: 'Fetch and convert web pages to markdown for reading and analysis',
-  category: 'utility',
-  command: 'npx',
-  args: ['-y', '@modelcontextprotocol/server-fetch'],
-  requiredEnvVars: [],
-  optionalEnvVars: [],
-  setupInstructions: 'No configuration required. Fetches web content and converts HTML to markdown.',
-  documentationUrl: 'https://github.com/modelcontextprotocol/servers/tree/main/src/fetch',
-};

src/shared/src/profiles/templates/filesystem.ts

@@ -1,16 +0,0 @@
-import type { ProfileTemplate } from '../types.js';
-
-export const filesystemTemplate: ProfileTemplate = {
-  id: 'filesystem',
-  name: 'filesystem',
-  displayName: 'Filesystem',
-  description: 'Provides read/write access to local filesystem directories',
-  category: 'filesystem',
-  command: 'npx',
-  args: ['-y', '@modelcontextprotocol/server-filesystem'],
-  requiredEnvVars: [],
-  optionalEnvVars: [],
-  setupInstructions:
-    'Append allowed directory paths as additional args. Example: npx -y @modelcontextprotocol/server-filesystem /home/user/docs',
-  documentationUrl: 'https://github.com/modelcontextprotocol/servers/tree/main/src/filesystem',
-};

src/shared/src/profiles/templates/github.ts

@@ -1,22 +0,0 @@
-import type { ProfileTemplate } from '../types.js';
-
-export const githubTemplate: ProfileTemplate = {
-  id: 'github',
-  name: 'github',
-  displayName: 'GitHub',
-  description: 'Interact with GitHub repositories, issues, pull requests, and more',
-  category: 'integration',
-  command: 'npx',
-  args: ['-y', '@modelcontextprotocol/server-github'],
-  requiredEnvVars: [
-    {
-      name: 'GITHUB_PERSONAL_ACCESS_TOKEN',
-      description: 'GitHub personal access token with repo scope',
-      isSecret: true,
-      setupUrl: 'https://github.com/settings/tokens',
-    },
-  ],
-  optionalEnvVars: [],
-  setupInstructions: 'Create a personal access token at GitHub Settings > Developer settings > Personal access tokens.',
-  documentationUrl: 'https://github.com/modelcontextprotocol/servers/tree/main/src/github',
-};

src/shared/src/profiles/templates/index.ts

@@ -1,6 +0,0 @@
-export { filesystemTemplate } from './filesystem.js';
-export { githubTemplate } from './github.js';
-export { postgresTemplate } from './postgres.js';
-export { slackTemplate } from './slack.js';
-export { memoryTemplate } from './memory.js';
-export { fetchTemplate } from './fetch.js';

src/shared/src/profiles/templates/memory.ts

@@ -1,15 +0,0 @@
-import type { ProfileTemplate } from '../types.js';
-
-export const memoryTemplate: ProfileTemplate = {
-  id: 'memory',
-  name: 'memory',
-  displayName: 'Memory',
-  description: 'Persistent knowledge graph memory for storing and retrieving entities and relations',
-  category: 'utility',
-  command: 'npx',
-  args: ['-y', '@modelcontextprotocol/server-memory'],
-  requiredEnvVars: [],
-  optionalEnvVars: [],
-  setupInstructions: 'No configuration required. Memory is stored locally in a JSON knowledge graph file.',
-  documentationUrl: 'https://github.com/modelcontextprotocol/servers/tree/main/src/memory',
-};

src/shared/src/profiles/templates/postgres.ts

@@ -1,21 +0,0 @@
-import type { ProfileTemplate } from '../types.js';
-
-export const postgresTemplate: ProfileTemplate = {
-  id: 'postgres',
-  name: 'postgres',
-  displayName: 'PostgreSQL',
-  description: 'Query and inspect PostgreSQL databases with read-only access',
-  category: 'database',
-  command: 'npx',
-  args: ['-y', '@modelcontextprotocol/server-postgres'],
-  requiredEnvVars: [
-    {
-      name: 'DATABASE_URL',
-      description: 'PostgreSQL connection string (e.g., postgresql://user:pass@localhost:5432/dbname)',
-      isSecret: true,
-    },
-  ],
-  optionalEnvVars: [],
-  setupInstructions: 'Provide a PostgreSQL connection string. The server provides read-only query access by default.',
-  documentationUrl: 'https://github.com/modelcontextprotocol/servers/tree/main/src/postgres',
-};

src/shared/src/profiles/templates/slack.ts

@@ -1,28 +0,0 @@
-import type { ProfileTemplate } from '../types.js';
-
-export const slackTemplate: ProfileTemplate = {
-  id: 'slack',
-  name: 'slack',
-  displayName: 'Slack',
-  description: 'Read and send Slack messages, manage channels, and search workspace content',
-  category: 'integration',
-  command: 'npx',
-  args: ['-y', '@modelcontextprotocol/server-slack'],
-  requiredEnvVars: [
-    {
-      name: 'SLACK_BOT_TOKEN',
-      description: 'Slack Bot User OAuth Token (starts with xoxb-)',
-      isSecret: true,
-      setupUrl: 'https://api.slack.com/apps',
-    },
-    {
-      name: 'SLACK_TEAM_ID',
-      description: 'Slack workspace/team ID',
-      isSecret: false,
-    },
-  ],
-  optionalEnvVars: [],
-  setupInstructions:
-    'Create a Slack App at api.slack.com/apps, install it to your workspace, and copy the Bot User OAuth Token.',
-  documentationUrl: 'https://github.com/modelcontextprotocol/servers/tree/main/src/slack',
-};

src/shared/src/profiles/types.ts

@@ -1,35 +0,0 @@
-import { z } from 'zod';
-
-export const envTemplateEntrySchema = z.object({
-  name: z.string().min(1),
-  description: z.string(),
-  isSecret: z.boolean(),
-  setupUrl: z.string().url().optional(),
-  defaultValue: z.string().optional(),
-});
-
-export const profileTemplateSchema = z.object({
-  id: z.string().min(1).regex(/^[a-z0-9-]+$/, 'ID must be lowercase alphanumeric with hyphens'),
-  name: z.string().min(1),
-  displayName: z.string().min(1),
-  description: z.string().min(1),
-  category: z.enum(['filesystem', 'database', 'integration', 'ai', 'utility', 'development']),
-  command: z.string().min(1),
-  args: z.array(z.string()),
-  requiredEnvVars: z.array(envTemplateEntrySchema).default([]),
-  optionalEnvVars: z.array(envTemplateEntrySchema).default([]),
-  setupInstructions: z.string().optional(),
-  documentationUrl: z.string().url().optional(),
-});
-
-export type ProfileTemplate = z.infer<typeof profileTemplateSchema>;
-
-export type ProfileCategory = ProfileTemplate['category'];
-
-export interface InstantiatedProfile {
-  name: string;
-  templateId: string;
-  command: string;
-  args: string[];
-  env: Record<string, string>;
-}

src/shared/src/profiles/utils.ts

@@ -1,61 +0,0 @@
-import { profileTemplateSchema } from './types.js';
-import type { ProfileTemplate, InstantiatedProfile } from './types.js';
-
-export function validateTemplate(template: unknown): { success: true; data: ProfileTemplate } | { success: false; errors: string[] } {
-  const result = profileTemplateSchema.safeParse(template);
-  if (result.success) {
-    return { success: true, data: result.data };
-  }
-  return {
-    success: false,
-    errors: result.error.issues.map((i) => `${i.path.join('.')}: ${i.message}`),
-  };
-}
-
-export function getMissingEnvVars(template: ProfileTemplate, envValues: Record<string, string>): string[] {
-  return template.requiredEnvVars
-    .filter((e) => !envValues[e.name] && e.defaultValue === undefined)
-    .map((e) => e.name);
-}
-
-export function instantiateProfile(
-  template: ProfileTemplate,
-  envValues: Record<string, string>,
-): InstantiatedProfile {
-  const missing = getMissingEnvVars(template, envValues);
-  if (missing.length > 0) {
-    throw new Error(`Missing required environment variables: ${missing.join(', ')}`);
-  }
-
-  const env: Record<string, string> = {};
-  for (const entry of template.requiredEnvVars) {
-    const value = envValues[entry.name] ?? entry.defaultValue;
-    if (value !== undefined) {
-      env[entry.name] = value;
-    }
-  }
-  for (const entry of template.optionalEnvVars) {
-    const value = envValues[entry.name] ?? entry.defaultValue;
-    if (value !== undefined) {
-      env[entry.name] = value;
-    }
-  }
-
-  return {
-    name: template.name,
-    templateId: template.id,
-    command: template.command,
-    args: [...template.args],
-    env,
-  };
-}
-
-export function generateMcpJsonEntry(profile: InstantiatedProfile): Record<string, unknown> {
-  return {
-    [profile.name]: {
-      command: profile.command,
-      args: profile.args,
-      env: profile.env,
-    },
-  };
-}

src/shared/src/types/index.ts

@@ -6,29 +6,19 @@ export interface McpServerConfig {
   type: string;
   command: string;
   args: string[];
-  envTemplate: EnvTemplateEntry[];
+  env: EnvEntry[];
   setupGuide?: string;
 }
 
-export interface EnvTemplateEntry {
+export interface EnvEntry {
   name: string;
-  description: string;
-  isSecret: boolean;
-  setupUrl?: string;
-  defaultValue?: string;
-}
-
-export interface McpProfile {
-  name: string;
-  serverId: string;
-  config: Record<string, unknown>;
-  filterRules?: Record<string, unknown>;
+  value?: string;
+  valueFrom?: { secretRef: { name: string; key: string } };
 }
 
 export interface McpProject {
   name: string;
   description?: string;
-  profileIds: string[];
 }
 
 // Service interfaces for dependency injection