fix: keep stdin open for STDIO servers + describe instance resolves server names

STDIO MCP servers read from stdin and exit on EOF. Docker containers close
stdin by default, causing all STDIO servers to crash immediately. Added
OpenStdin: true to container creation.

Describe instance now resolves server names (like logs command), preferring
RUNNING instances. Added 7 new describe tests covering server name resolution,
healthcheck display, events section, and template detail.

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

.gitignore

@@ -9,6 +9,8 @@ dist/
 .env
 .env.local
 .env.*.local
+stack/.env
+.portainer_password
 
 # Logs
 logs/

deploy.sh

@@ -0,0 +1,398 @@
+#!/bin/bash
+# Deploy mcpctl stack to Portainer
+# Usage: ./deploy.sh [--dry-run]
+
+set -e
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+STACK_DIR="$SCRIPT_DIR/stack"
+COMPOSE_FILE="$STACK_DIR/docker-compose.yml"
+ENV_FILE="$STACK_DIR/.env"
+
+# Portainer configuration
+PORTAINER_URL="${PORTAINER_URL:-http://10.0.0.194:9000}"
+PORTAINER_USER="${PORTAINER_USER:-michal}"
+STACK_NAME="mcpctl"
+ENDPOINT_ID="2"
+
+# Colors for output
+RED='\033[0;31m'
+GREEN='\033[0;32m'
+YELLOW='\033[1;33m'
+NC='\033[0m'
+
+log_info() { echo -e "${GREEN}[INFO]${NC} $1" >&2; }
+log_warn() { echo -e "${YELLOW}[WARN]${NC} $1" >&2; }
+log_error() { echo -e "${RED}[ERROR]${NC} $1" >&2; }
+
+check_files() {
+    if [[ ! -f "$COMPOSE_FILE" ]]; then
+        log_error "Compose file not found: $COMPOSE_FILE"
+        exit 1
+    fi
+    if [[ ! -f "$ENV_FILE" ]]; then
+        log_error "Environment file not found: $ENV_FILE"
+        exit 1
+    fi
+    log_info "Found compose file: $COMPOSE_FILE"
+    log_info "Found env file: $ENV_FILE"
+}
+
+get_password() {
+    if [[ -n "$PORTAINER_PASSWORD" ]]; then
+        echo "$PORTAINER_PASSWORD"
+        return
+    fi
+    if [[ -f "$SCRIPT_DIR/.portainer_password" ]]; then
+        cat "$SCRIPT_DIR/.portainer_password"
+        return
+    fi
+    if [[ -f "$HOME/.portainer_password" ]]; then
+        cat "$HOME/.portainer_password"
+        return
+    fi
+    read -s -p "Enter Portainer password for $PORTAINER_USER: " password
+    echo >&2
+    echo "$password"
+}
+
+get_jwt_token() {
+    local password="$1"
+    log_info "Authenticating to Portainer..."
+
+    local escaped_password
+    escaped_password=$(printf '%s' "$password" | jq -Rs .)
+
+    local response
+    response=$(curl -s -X POST "$PORTAINER_URL/api/auth" \
+        -H "Content-Type: application/json" \
+        -d "{\"Username\":\"$PORTAINER_USER\",\"Password\":$escaped_password}")
+
+    local token
+    token=$(echo "$response" | jq -r '.jwt // empty')
+
+    if [[ -z "$token" ]]; then
+        log_error "Authentication failed: $(echo "$response" | jq -r '.message // "Unknown error"')"
+        exit 1
+    fi
+    echo "$token"
+}
+
+parse_env_to_json() {
+    local env_file="$1"
+    local json_array="["
+    local first=true
+
+    while IFS= read -r line || [[ -n "$line" ]]; do
+        [[ "$line" =~ ^#.*$ ]] && continue
+        [[ -z "$line" ]] && continue
+
+        local name="${line%%=*}"
+        local value="${line#*=}"
+        [[ "$name" == "$line" ]] && continue
+
+        if [[ "$first" == "true" ]]; then
+            first=false
+        else
+            json_array+=","
+        fi
+
+        value=$(echo "$value" | sed 's/\\/\\\\/g; s/"/\\"/g')
+        json_array+="{\"name\":\"$name\",\"value\":\"$value\"}"
+    done < "$env_file"
+
+    json_array+="]"
+    echo "$json_array"
+}
+
+# Find existing stack by name
+find_stack_id() {
+    local token="$1"
+    local response
+    response=$(curl -s -X GET "$PORTAINER_URL/api/stacks" \
+        -H "Authorization: Bearer $token")
+
+    echo "$response" | jq -r --arg name "$STACK_NAME" \
+        '.[] | select(.Name == $name) | .Id // empty'
+}
+
+get_stack_info() {
+    local token="$1"
+    local stack_id="$2"
+    curl -s -X GET "$PORTAINER_URL/api/stacks/$stack_id" \
+        -H "Authorization: Bearer $token" \
+        -H "Content-Type: application/json"
+}
+
+get_stack_file() {
+    local token="$1"
+    local stack_id="$2"
+    local response
+    response=$(curl -s -X GET "$PORTAINER_URL/api/stacks/$stack_id/file" \
+        -H "Authorization: Bearer $token" \
+        -H "Content-Type: application/json")
+
+    if echo "$response" | jq -e '.StackFileContent' > /dev/null 2>&1; then
+        echo "$response" | jq -r '.StackFileContent'
+    else
+        echo "# Could not retrieve current compose file"
+    fi
+}
+
+show_diff() {
+    local token="$1"
+    local stack_id="$2"
+    local env_json="$3"
+
+    log_info "Fetching current state from Portainer..."
+
+    local current_compose
+    current_compose=$(get_stack_file "$token" "$stack_id")
+
+    local current_env
+    local stack_info
+    stack_info=$(get_stack_info "$token" "$stack_id")
+    current_env=$(echo "$stack_info" | jq -r 'if .Env then .Env[] | "\(.name)=\(.value)" else empty end' 2>/dev/null | sort)
+
+    local new_env
+    new_env=$(echo "$env_json" | jq -r '.[] | "\(.name)=\(.value)"' | sort)
+
+    local tmp_dir
+    tmp_dir=$(mktemp -d)
+
+    echo "$current_compose" > "$tmp_dir/current_compose.yml"
+    cat "$COMPOSE_FILE" > "$tmp_dir/new_compose.yml"
+    echo "$current_env" > "$tmp_dir/current_env.txt"
+    echo "$new_env" > "$tmp_dir/new_env.txt"
+
+    echo ""
+    echo "=== ENVIRONMENT VARIABLES DIFF ==="
+    echo ""
+
+    if diff -u "$tmp_dir/current_env.txt" "$tmp_dir/new_env.txt" > "$tmp_dir/env_diff.txt" 2>&1; then
+        echo -e "${GREEN}No changes in environment variables${NC}"
+    else
+        while IFS= read -r line; do
+            if [[ "$line" == ---* ]] || [[ "$line" == +++* ]] || [[ "$line" == @@* ]]; then
+                echo -e "${YELLOW}$line${NC}"
+            elif [[ "$line" == -* ]]; then
+                echo -e "${RED}$line${NC}"
+            elif [[ "$line" == +* ]]; then
+                echo -e "${GREEN}$line${NC}"
+            else
+                echo "$line"
+            fi
+        done < "$tmp_dir/env_diff.txt"
+    fi
+
+    echo ""
+    echo "=== COMPOSE FILE DIFF ==="
+    echo ""
+
+    if diff -u "$tmp_dir/current_compose.yml" "$tmp_dir/new_compose.yml" > "$tmp_dir/compose_diff.txt" 2>&1; then
+        echo -e "${GREEN}No changes in compose file${NC}"
+    else
+        while IFS= read -r line; do
+            if [[ "$line" == ---* ]] || [[ "$line" == +++* ]] || [[ "$line" == @@* ]]; then
+                echo -e "${YELLOW}$line${NC}"
+            elif [[ "$line" == -* ]]; then
+                echo -e "${RED}$line${NC}"
+            elif [[ "$line" == +* ]]; then
+                echo -e "${GREEN}$line${NC}"
+            else
+                echo "$line"
+            fi
+        done < "$tmp_dir/compose_diff.txt"
+    fi
+
+    rm -rf "$tmp_dir"
+}
+
+create_stack() {
+    local token="$1"
+    local env_json="$2"
+
+    local compose_content
+    compose_content=$(cat "$COMPOSE_FILE")
+
+    local compose_escaped
+    compose_escaped=$(echo "$compose_content" | jq -Rs .)
+
+    log_info "Creating new stack '$STACK_NAME'..."
+
+    local payload
+    payload=$(jq -n \
+        --arg name "$STACK_NAME" \
+        --argjson env "$env_json" \
+        --argjson stackFileContent "$compose_escaped" \
+        '{
+            "name": $name,
+            "env": $env,
+            "stackFileContent": $stackFileContent
+        }')
+
+    local response
+    response=$(curl -s -X POST "$PORTAINER_URL/api/stacks?type=2&method=string&endpointId=$ENDPOINT_ID" \
+        -H "Authorization: Bearer $token" \
+        -H "Content-Type: application/json" \
+        -d "$payload")
+
+    local error_msg
+    error_msg=$(echo "$response" | jq -r '.message // empty')
+
+    if [[ -n "$error_msg" ]]; then
+        log_error "Stack creation failed: $error_msg"
+        echo "$response" | jq .
+        exit 1
+    fi
+
+    local new_id
+    new_id=$(echo "$response" | jq -r '.Id')
+    log_info "Stack created successfully! (ID: $new_id)"
+    echo "$response" | jq '{Id, Name, Status, CreationDate}'
+}
+
+update_stack() {
+    local token="$1"
+    local stack_id="$2"
+    local dry_run="$3"
+
+    local compose_content
+    compose_content=$(cat "$COMPOSE_FILE")
+
+    local env_json
+    env_json=$(parse_env_to_json "$ENV_FILE")
+
+    if [[ "$dry_run" == "true" ]]; then
+        log_warn "DRY RUN - Not actually deploying"
+        show_diff "$token" "$stack_id" "$env_json"
+        echo ""
+        log_warn "DRY RUN complete - no changes made"
+        log_info "Run without --dry-run to apply these changes"
+        return 0
+    fi
+
+    local env_count
+    env_count=$(echo "$env_json" | jq 'length')
+    log_info "Deploying $env_count environment variables"
+    log_info "Updating stack '$STACK_NAME' (ID: $stack_id)..."
+
+    local compose_escaped
+    compose_escaped=$(echo "$compose_content" | jq -Rs .)
+
+    local payload
+    payload=$(jq -n \
+        --argjson env "$env_json" \
+        --argjson stackFileContent "$compose_escaped" \
+        '{
+            "env": $env,
+            "stackFileContent": $stackFileContent,
+            "prune": true,
+            "pullImage": true
+        }')
+
+    local response
+    response=$(curl -s -X PUT "$PORTAINER_URL/api/stacks/$stack_id?endpointId=$ENDPOINT_ID" \
+        -H "Authorization: Bearer $token" \
+        -H "Content-Type: application/json" \
+        -d "$payload")
+
+    local error_msg
+    error_msg=$(echo "$response" | jq -r '.message // empty')
+
+    if [[ -n "$error_msg" ]]; then
+        log_error "Deployment failed: $error_msg"
+        echo "$response" | jq .
+        exit 1
+    fi
+
+    log_info "Stack updated successfully!"
+    echo "$response" | jq '{Id, Name, Status, CreationDate, UpdateDate}'
+}
+
+main() {
+    local dry_run=false
+
+    while [[ $# -gt 0 ]]; do
+        case $1 in
+            --dry-run)
+                dry_run=true
+                shift
+                ;;
+            --help|-h)
+                echo "Usage: $0 [--dry-run]"
+                echo ""
+                echo "Deploy mcpctl stack to Portainer"
+                echo ""
+                echo "Options:"
+                echo "  --dry-run    Show what would be deployed without actually deploying"
+                echo "  --help       Show this help message"
+                echo ""
+                echo "Environment variables:"
+                echo "  PORTAINER_URL       Portainer URL (default: http://10.0.0.194:9000)"
+                echo "  PORTAINER_USER      Portainer username (default: michal)"
+                echo "  PORTAINER_PASSWORD  Portainer password (or store in ~/.portainer_password)"
+                exit 0
+                ;;
+            *)
+                log_error "Unknown option: $1"
+                exit 1
+                ;;
+        esac
+    done
+
+    echo "========================================"
+    echo "  mcpctl Stack Deployment"
+    echo "========================================"
+    echo ""
+
+    check_files
+
+    local password
+    password=$(get_password)
+
+    local token
+    token=$(get_jwt_token "$password")
+    log_info "Authentication successful"
+
+    # Find or create stack
+    local stack_id
+    stack_id=$(find_stack_id "$token")
+
+    if [[ -z "$stack_id" ]]; then
+        if [[ "$dry_run" == "true" ]]; then
+            log_warn "Stack '$STACK_NAME' does not exist yet"
+            log_info "A real deploy would create it"
+            return 0
+        fi
+
+        log_info "Stack '$STACK_NAME' not found, creating..."
+        local env_json
+        env_json=$(parse_env_to_json "$ENV_FILE")
+        create_stack "$token" "$env_json"
+    else
+        local stack_info
+        stack_info=$(get_stack_info "$token" "$stack_id")
+        local status_code
+        status_code=$(echo "$stack_info" | jq -r '.Status // 0')
+        local status_text="Unknown"
+        case "$status_code" in
+            1) status_text="Active" ;;
+            2) status_text="Inactive" ;;
+        esac
+        log_info "Current stack status: $status_text (ID: $stack_id, Env vars: $(echo "$stack_info" | jq '.Env | length'))"
+
+        echo ""
+        update_stack "$token" "$stack_id" "$dry_run"
+    fi
+
+    echo ""
+    log_info "Done!"
+
+    if [[ "$dry_run" == "false" ]]; then
+        log_info "Check Portainer UI to verify containers are running"
+        log_info "URL: $PORTAINER_URL/#!/$ENDPOINT_ID/docker/stacks/$STACK_NAME"
+    fi
+}
+
+main "$@"

deploy/Dockerfile.mcpd

@@ -49,6 +49,9 @@ COPY --from=builder /app/src/shared/dist/ src/shared/dist/
 COPY --from=builder /app/src/db/dist/ src/db/dist/
 COPY --from=builder /app/src/mcpd/dist/ src/mcpd/dist/
 
+# Copy templates for seeding
+COPY templates/ templates/
+
 # Copy entrypoint
 COPY deploy/entrypoint.sh /entrypoint.sh
 RUN chmod +x /entrypoint.sh

deploy/Dockerfile.node-runner

@@ -0,0 +1,13 @@
+# Base container for npm-based MCP servers (STDIO transport).
+# mcpd uses this image to run `npx -y <packageName>` when a server
+# has packageName but no dockerImage.
+# Using slim (Debian) instead of alpine for better npm package compatibility.
+FROM node:20-slim
+
+WORKDIR /mcp
+
+# Pre-warm npx cache directory
+RUN mkdir -p /root/.npm
+
+# Default entrypoint — overridden by mcpd via container command
+ENTRYPOINT ["npx", "-y"]

deploy/docker-compose.yml

@@ -30,6 +30,8 @@ services:
       MCPD_PORT: "3100"
       MCPD_HOST: "0.0.0.0"
       MCPD_LOG_LEVEL: info
+      MCPD_NODE_RUNNER_IMAGE: mcpctl-node-runner:latest
+      MCPD_MCP_NETWORK: mcp-servers
     depends_on:
       postgres:
         condition: service_healthy
@@ -48,6 +50,16 @@ services:
       retries: 3
       start_period: 10s
 
+  # Base image for npm-based MCP servers (built once, used by mcpd)
+  node-runner:
+    build:
+      context: ..
+      dockerfile: deploy/Dockerfile.node-runner
+    image: mcpctl-node-runner:latest
+    profiles:
+      - build
+    entrypoint: ["echo", "Image built successfully"]
+
   postgres-test:
     image: postgres:16-alpine
     container_name: mcpctl-postgres-test
@@ -71,8 +83,11 @@ networks:
   mcpctl:
     driver: bridge
   mcp-servers:
+    name: mcp-servers
     driver: bridge
-    internal: true
+    # Not internal — MCP servers need outbound access to reach external APIs
+    # (e.g., Grafana, Home Assistant). Isolation is enforced by not binding
+    # host ports on MCP server containers; only mcpd can reach them.
 
 volumes:
   mcpctl-pgdata:

deploy/entrypoint.sh

@@ -4,8 +4,8 @@ set -e
 echo "mcpd: pushing database schema..."
 pnpm -F @mcpctl/db exec prisma db push --schema=prisma/schema.prisma --accept-data-loss 2>&1
 
-echo "mcpd: seeding default data..."
-node src/mcpd/dist/seed-runner.js
+echo "mcpd: seeding templates..."
+TEMPLATES_DIR=templates node src/mcpd/dist/seed-runner.js
 
 echo "mcpd: starting server..."
 exec node src/mcpd/dist/main.js

deploy/mcplocal.service

@@ -0,0 +1,15 @@
+[Unit]
+Description=mcpctl local MCP proxy
+After=network.target
+
+[Service]
+Type=simple
+ExecStart=/usr/bin/mcpctl-local
+Restart=on-failure
+RestartSec=5
+Environment=MCPLOCAL_MCPD_URL=http://10.0.0.194:3100
+Environment=MCPLOCAL_HTTP_PORT=3200
+Environment=MCPLOCAL_HTTP_HOST=127.0.0.1
+
+[Install]
+WantedBy=default.target

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

@@ -11,12 +11,14 @@ servers:
       - "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"
-    envTemplate:
+    env:
       - name: HOMEASSISTANT_URL
-        description: "Home Assistant instance URL (e.g. https://ha.example.com)"
+        value: ""
       - name: HOMEASSISTANT_TOKEN
-        description: "Home Assistant long-lived access token"
-        isSecret: true
+        valueFrom:
+          secretRef:
+            name: ha-secrets
+            key: token
 
 profiles:
   - name: production

installlocal.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+# Build (if needed) and install mcpctl RPM locally
+set -e
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+cd "$SCRIPT_DIR"
+
+RPM_FILE=$(ls dist/mcpctl-*.rpm 2>/dev/null | head -1)
+
+# Build if no RPM exists or if source is newer than the RPM
+if [[ -z "$RPM_FILE" ]] || [[ $(find src/ -name '*.ts' -newer "$RPM_FILE" 2>/dev/null | head -1) ]]; then
+    echo "==> Building RPM..."
+    bash scripts/build-rpm.sh
+    RPM_FILE=$(ls dist/mcpctl-*.rpm 2>/dev/null | head -1)
+else
+    echo "==> RPM is up to date: $RPM_FILE"
+fi
+
+echo "==> Installing $RPM_FILE..."
+sudo rpm -Uvh --force "$RPM_FILE"
+
+echo "==> Reloading systemd user units..."
+systemctl --user daemon-reload
+
+echo "==> Done!"
+echo "    Enable mcplocal: systemctl --user enable --now mcplocal"

nfpm.yaml

@@ -10,6 +10,14 @@ contents:
     dst: /usr/bin/mcpctl
     file_info:
       mode: 0755
+  - src: ./dist/mcpctl-local
+    dst: /usr/bin/mcpctl-local
+    file_info:
+      mode: 0755
+  - src: ./deploy/mcplocal.service
+    dst: /usr/lib/systemd/user/mcplocal.service
+    file_info:
+      mode: 0644
   - src: ./completions/mcpctl.bash
     dst: /usr/share/bash-completion/completions/mcpctl
     file_info:

package.json

@@ -18,7 +18,11 @@
     "typecheck": "tsc --build",
     "rpm:build": "bash scripts/build-rpm.sh",
     "rpm:publish": "bash scripts/publish-rpm.sh",
-    "release": "bash scripts/release.sh"
+    "release": "bash scripts/release.sh",
+    "mcpd:build": "bash scripts/build-mcpd.sh",
+    "mcpd:deploy": "bash deploy.sh",
+    "mcpd:deploy-dry": "bash deploy.sh --dry-run",
+    "mcpd:logs": "bash logs.sh"
   },
   "engines": {
     "node": ">=20.0.0",

pnpm-lock.yaml

@@ -112,6 +112,9 @@ importers:
       fastify:
         specifier: ^5.0.0
         version: 5.7.4
+      js-yaml:
+        specifier: ^4.1.0
+        version: 4.1.1
       zod:
         specifier: ^3.24.0
         version: 3.25.76
@@ -122,6 +125,9 @@ importers:
       '@types/dockerode':
         specifier: ^4.0.1
         version: 4.0.1
+      '@types/js-yaml':
+        specifier: ^4.0.9
+        version: 4.0.9
       '@types/node':
         specifier: ^25.3.0
         version: 25.3.0

scripts/build-mcpd.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+# Build mcpd Docker image and push to Gitea container registry
+set -e
+
+SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
+PROJECT_ROOT="$(dirname "$SCRIPT_DIR")"
+cd "$PROJECT_ROOT"
+
+# Load .env for GITEA_TOKEN
+if [ -f .env ]; then
+  set -a; source .env; set +a
+fi
+
+# Push directly to internal address (external proxy has body size limit)
+REGISTRY="10.0.0.194:3012"
+IMAGE="mcpd"
+TAG="${1:-latest}"
+
+echo "==> Building mcpd image..."
+podman build -t "$IMAGE:$TAG" -f deploy/Dockerfile.mcpd .
+
+echo "==> Tagging as $REGISTRY/michal/$IMAGE:$TAG..."
+podman tag "$IMAGE:$TAG" "$REGISTRY/michal/$IMAGE:$TAG"
+
+echo "==> Logging in to $REGISTRY..."
+podman login --tls-verify=false -u michal -p "$GITEA_TOKEN" "$REGISTRY"
+
+echo "==> Pushing to $REGISTRY/michal/$IMAGE:$TAG..."
+podman push --tls-verify=false "$REGISTRY/michal/$IMAGE:$TAG"
+
+echo "==> Done!"
+echo "    Image: $REGISTRY/michal/$IMAGE:$TAG"

scripts/build-rpm.sh

@@ -16,10 +16,11 @@ export PATH="$HOME/.npm-global/bin:$HOME/.bun/bin:$HOME/.local/bin:$PATH"
 echo "==> Building TypeScript..."
 pnpm build
 
-echo "==> Bundling standalone binary..."
+echo "==> Bundling standalone binaries..."
 mkdir -p dist
-rm -f dist/mcpctl dist/mcpctl-*.rpm
+rm -f dist/mcpctl dist/mcpctl-local dist/mcpctl-*.rpm
 bun build src/cli/src/index.ts --compile --outfile dist/mcpctl
+bun build src/mcplocal/src/main.ts --compile --outfile dist/mcpctl-local
 
 echo "==> Packaging RPM..."
 nfpm pkg --packager rpm --target dist/

src/cli/src/commands/apply.ts

@@ -4,6 +4,22 @@ import yaml from 'js-yaml';
 import { z } from 'zod';
 import type { ApiClient } from '../api-client.js';
 
+const HealthCheckSchema = z.object({
+  tool: z.string().min(1),
+  arguments: z.record(z.unknown()).default({}),
+  intervalSeconds: z.number().int().min(5).max(3600).default(60),
+  timeoutSeconds: z.number().int().min(1).max(120).default(10),
+  failureThreshold: z.number().int().min(1).max(20).default(3),
+});
+
+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(''),
@@ -15,30 +31,48 @@ const ServerSpecSchema = z.object({
   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),
-  envTemplate: z.array(z.object({
-    name: z.string(),
-    description: z.string().default(''),
-    isSecret: z.boolean().default(false),
-  })).default([]),
+  env: z.array(ServerEnvEntrySchema).default([]),
+  healthCheck: HealthCheckSchema.optional(),
 });
 
-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 TemplateEnvEntrySchema = z.object({
+  name: z.string().min(1),
+  description: z.string().optional(),
+  required: z.boolean().optional(),
+  defaultValue: z.string().optional(),
+});
+
+const TemplateSpecSchema = z.object({
+  name: z.string().min(1),
+  version: z.string().default('1.0.0'),
+  description: z.string().default(''),
+  packageName: z.string().optional(),
+  dockerImage: z.string().optional(),
+  transport: z.enum(['STDIO', 'SSE', 'STREAMABLE_HTTP']).default('STDIO'),
+  repositoryUrl: z.string().optional(),
+  externalUrl: z.string().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(TemplateEnvEntrySchema).default([]),
+  healthCheck: HealthCheckSchema.optional(),
 });
 
 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([]),
+  templates: z.array(TemplateSpecSchema).default([]),
 });
 
 export type ApplyConfig = z.infer<typeof ApplyConfigSchema>;
@@ -61,8 +95,9 @@ 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)`);
+        if (config.templates.length > 0) log(`  ${config.templates.length} template(s)`);
         return;
       }
 
@@ -84,7 +119,7 @@ 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);
@@ -100,34 +135,19 @@ 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}`);
     }
   }
 
@@ -151,6 +171,22 @@ async function applyConfig(client: ApiClient, config: ApplyConfig, log: (...args
       log(`Error applying project '${project.name}': ${err instanceof Error ? err.message : err}`);
     }
   }
+
+  // Apply templates
+  for (const template of config.templates) {
+    try {
+      const existing = await findByName(client, 'templates', template.name);
+      if (existing) {
+        await client.put(`/api/v1/templates/${(existing as { id: string }).id}`, template);
+        log(`Updated template: ${template.name}`);
+      } else {
+        await client.post('/api/v1/templates', template);
+        log(`Created template: ${template.name}`);
+      }
+    } catch (err) {
+      log(`Error applying template '${template.name}': ${err instanceof Error ? err.message : err}`);
+    }
+  }
 }
 
 async function findByName(client: ApiClient, resource: string, name: string): Promise<unknown | null> {
@@ -162,16 +198,5 @@ 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

@@ -1,7 +1,5 @@
 import { Command } from 'commander';
-import type { ApiClient } from '../api-client.js';
-import { resolveNameOrId } from './shared.js';
-
+import { type ApiClient, ApiError } from '../api-client.js';
 export interface CreateCommandDeps {
   client: ApiClient;
   log: (...args: unknown[]) => void;
@@ -11,17 +9,33 @@ function collect(value: string, prev: string[]): string[] {
   return [...prev, value];
 }
 
-function parseEnvTemplate(entries: string[]): Array<{ name: string; description: string; isSecret: boolean }> {
+interface ServerEnvEntry {
+  name: string;
+  value?: string;
+  valueFrom?: { secretRef: { name: string; key: string } };
+}
+
+function parseServerEnv(entries: string[]): ServerEnvEntry[] {
   return entries.map((entry) => {
-    const parts = entry.split(':');
-    if (parts.length < 2) {
-      throw new Error(`Invalid env-template format '${entry}'. Expected NAME:description[:isSecret]`);
+    const eqIdx = entry.indexOf('=');
+    if (eqIdx === -1) {
+      throw new Error(`Invalid env format '${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: parts[0]!,
-      description: parts[1]!,
-      isSecret: parts[2] === 'true',
+        name: envName,
+        valueFrom: { secretRef: { name: parts[1]!, key: parts[2]! } },
       };
+    }
+
+    return { name: envName, value: rhs };
   });
 }
 
@@ -41,60 +55,139 @@ export function createCreateCommand(deps: CreateCommandDeps): Command {
   const { client, log } = deps;
 
   const cmd = new Command('create')
-    .description('Create a resource (server, profile, project)');
+    .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('-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('--transport <type>', 'Transport type (STDIO, SSE, STREAMABLE_HTTP)')
     .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-template <entry>', 'Env template (NAME:description[:isSecret], repeat for multiple)', collect, [])
+    .option('--replicas <count>', 'Number of replicas')
+    .option('--env <entry>', 'Env var: KEY=value (inline) or KEY=secretRef:SECRET:KEY (secret ref, repeat for multiple)', collect, [])
+    .option('--from-template <name>', 'Create from template (name or name:version)')
+    .option('--force', 'Update if already exists')
     .action(async (name: string, opts) => {
+      let base: Record<string, unknown> = {};
+
+      // If --from-template, fetch template and use as base
+      if (opts.fromTemplate) {
+        const tplRef = opts.fromTemplate as string;
+        const [tplName, tplVersion] = tplRef.includes(':')
+          ? [tplRef.slice(0, tplRef.indexOf(':')), tplRef.slice(tplRef.indexOf(':') + 1)]
+          : [tplRef, undefined];
+
+        const templates = await client.get<Array<Record<string, unknown>>>(`/api/v1/templates?name=${encodeURIComponent(tplName)}`);
+        let template: Record<string, unknown> | undefined;
+        if (tplVersion) {
+          template = templates.find((t) => t.name === tplName && t.version === tplVersion);
+          if (!template) throw new Error(`Template '${tplName}' version '${tplVersion}' not found`);
+        } else {
+          template = templates.find((t) => t.name === tplName);
+          if (!template) throw new Error(`Template '${tplName}' not found`);
+        }
+
+        // Copy template fields as base (strip template-only, internal, and null fields)
+        const { id: _id, createdAt: _c, updatedAt: _u, version: _v, name: _n, ...tplFields } = template;
+        base = {};
+        for (const [k, v] of Object.entries(tplFields)) {
+          if (v !== null && v !== undefined) base[k] = v;
+        }
+
+        // Convert template env (description/required) to server env (name/value/valueFrom)
+        const tplEnv = template.env as Array<{ name: string; description?: string; required?: boolean; defaultValue?: string }> | undefined;
+        if (tplEnv && tplEnv.length > 0) {
+          base.env = tplEnv.map((e) => ({ name: e.name, value: e.defaultValue ?? '' }));
+        }
+
+        // Track template origin
+        base.templateName = tplName;
+        base.templateVersion = (template.version as string) ?? '1.0.0';
+      }
+
+      // Build body: template base → CLI overrides (last wins)
       const body: Record<string, unknown> = {
+        ...base,
         name,
-        description: opts.description,
-        transport: opts.transport,
-        replicas: parseInt(opts.replicas, 10),
       };
+      if (opts.description !== undefined) body.description = opts.description;
+      if (opts.transport) body.transport = opts.transport;
+      if (opts.replicas) body.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.envTemplate.length > 0) body.envTemplate = parseEnvTemplate(opts.envTemplate);
+      if (opts.env.length > 0) {
+        // Merge: CLI env entries override template env entries by name
+        const cliEnv = parseServerEnv(opts.env);
+        const existing = (body.env as ServerEnvEntry[] | undefined) ?? [];
+        const merged = [...existing];
+        for (const entry of cliEnv) {
+          const idx = merged.findIndex((e) => e.name === entry.name);
+          if (idx >= 0) {
+            merged[idx] = entry;
+          } else {
+            merged.push(entry);
+          }
+        }
+        body.env = merged;
+      }
 
+      // Defaults when no template
+      if (!opts.fromTemplate) {
+        if (body.description === undefined) body.description = '';
+        if (!body.transport) body.transport = 'STDIO';
+        if (!body.replicas) body.replicas = 1;
+      }
+
+      try {
         const server = await client.post<{ id: string; name: string }>('/api/v1/servers', body);
         log(`server '${server.name}' created (id: ${server.id})`);
+      } catch (err) {
+        if (err instanceof ApiError && err.status === 409 && opts.force) {
+          const existing = (await client.get<Array<{ id: string; name: string }>>('/api/v1/servers')).find((s) => s.name === name);
+          if (!existing) throw err;
+          const { name: _n, ...updateBody } = body;
+          await client.put(`/api/v1/servers/${existing.id}`, updateBody);
+          log(`server '${name}' updated (id: ${existing.id})`);
+        } else {
+          throw err;
+        }
+      }
     });
 
-  // --- create profile ---
-  cmd.command('profile')
-    .description('Create a profile for an MCP server')
-    .argument('<name>', 'Profile name')
-    .requiredOption('--server <name-or-id>', 'Server name or ID')
-    .option('--permissions <perm>', 'Permission (repeat for multiple)', collect, [])
-    .option('--env <entry>', 'Environment override KEY=value (repeat for multiple)', collect, [])
+  // --- 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, [])
+    .option('--force', 'Update if already exists')
     .action(async (name: string, opts) => {
-      const serverId = await resolveNameOrId(client, 'servers', opts.server);
-
-      const body: Record<string, unknown> = {
+      const data = parseEnvEntries(opts.data);
+      try {
+        const secret = await client.post<{ id: string; name: string }>('/api/v1/secrets', {
           name,
-        serverId,
-      };
-      if (opts.permissions.length > 0) body.permissions = opts.permissions;
-      if (opts.env.length > 0) body.envOverrides = parseEnvEntries(opts.env);
-
-      const profile = await client.post<{ id: string; name: string }>('/api/v1/profiles', body);
-      log(`profile '${profile.name}' created (id: ${profile.id})`);
+          data,
+        });
+        log(`secret '${secret.name}' created (id: ${secret.id})`);
+      } catch (err) {
+        if (err instanceof ApiError && err.status === 409 && opts.force) {
+          const existing = (await client.get<Array<{ id: string; name: string }>>('/api/v1/secrets')).find((s) => s.name === name);
+          if (!existing) throw err;
+          await client.put(`/api/v1/secrets/${existing.id}`, { data });
+          log(`secret '${name}' updated (id: ${existing.id})`);
+        } else {
+          throw err;
+        }
+      }
     });
 
   // --- create project ---
@@ -102,12 +195,24 @@ export function createCreateCommand(deps: CreateCommandDeps): Command {
     .description('Create a project')
     .argument('<name>', 'Project name')
     .option('-d, --description <text>', 'Project description', '')
+    .option('--force', 'Update if already exists')
     .action(async (name: string, opts) => {
+      try {
         const project = await client.post<{ id: string; name: string }>('/api/v1/projects', {
           name,
           description: opts.description,
         });
         log(`project '${project.name}' created (id: ${project.id})`);
+      } catch (err) {
+        if (err instanceof ApiError && err.status === 409 && opts.force) {
+          const existing = (await client.get<Array<{ id: string; name: string }>>('/api/v1/projects')).find((p) => p.name === name);
+          if (!existing) throw err;
+          await client.put(`/api/v1/projects/${existing.id}`, { description: opts.description });
+          log(`project '${name}' updated (id: ${existing.id})`);
+        } else {
+          throw err;
+        }
+      }
     });
 
   return cmd;

src/cli/src/commands/describe.ts

@@ -34,17 +34,34 @@ function formatServerDetail(server: Record<string, unknown>): string {
     lines.push(`  ${command.join(' ')}`);
   }
 
-  const envTemplate = server.envTemplate as Array<{ name: string; description: string; isSecret?: boolean }> | undefined;
-  if (envTemplate && envTemplate.length > 0) {
+  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 Template:');
-    const nameW = Math.max(6, ...envTemplate.map((e) => e.name.length)) + 2;
-    const descW = Math.max(12, ...envTemplate.map((e) => e.description.length)) + 2;
-    lines.push(`  ${'NAME'.padEnd(nameW)}${'DESCRIPTION'.padEnd(descW)}SECRET`);
-    for (const env of envTemplate) {
-      lines.push(`  ${env.name.padEnd(nameW)}${env.description.padEnd(descW)}${env.isSecret ? 'yes' : 'no'}`);
+    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}`);
       }
     }
+  }
+
+  const hc = server.healthCheck as { tool: string; arguments?: Record<string, unknown>; intervalSeconds?: number; timeoutSeconds?: number; failureThreshold?: number } | null;
+  if (hc) {
+    lines.push('');
+    lines.push('Health Check:');
+    lines.push(`  ${pad('Tool:', 22)}${hc.tool}`);
+    if (hc.arguments && Object.keys(hc.arguments).length > 0) {
+      lines.push(`  ${pad('Arguments:', 22)}${JSON.stringify(hc.arguments)}`);
+    }
+    lines.push(`  ${pad('Interval:', 22)}${hc.intervalSeconds ?? 60}s`);
+    lines.push(`  ${pad('Timeout:', 22)}${hc.timeoutSeconds ?? 10}s`);
+    lines.push(`  ${pad('Failure Threshold:', 22)}${hc.failureThreshold ?? 3}`);
+  }
 
   lines.push('');
   lines.push('Metadata:');
@@ -57,12 +74,23 @@ function formatServerDetail(server: Record<string, unknown>): string {
 
 function formatInstanceDetail(instance: Record<string, unknown>, inspect?: Record<string, unknown>): string {
   const lines: string[] = [];
-  lines.push(`=== Instance: ${instance.id} ===`);
+  const server = instance.server as { name: string } | undefined;
+  lines.push(`=== Instance: ${server?.name ?? instance.id} ===`);
   lines.push(`${pad('Status:')}${instance.status}`);
-  lines.push(`${pad('Server ID:')}${instance.serverId}`);
+  lines.push(`${pad('Server:')}${server?.name ?? String(instance.serverId)}`);
   lines.push(`${pad('Container ID:')}${instance.containerId ?? '-'}`);
   lines.push(`${pad('Port:')}${instance.port ?? '-'}`);
 
+  // Health section
+  const healthStatus = instance.healthStatus as string | null;
+  const lastHealthCheck = instance.lastHealthCheck as string | null;
+  if (healthStatus || lastHealthCheck) {
+    lines.push('');
+    lines.push('Health:');
+    lines.push(`  ${pad('Status:', 16)}${healthStatus ?? 'unknown'}`);
+    if (lastHealthCheck) lines.push(`  ${pad('Last Check:', 16)}${lastHealthCheck}`);
+  }
+
   const metadata = instance.metadata as Record<string, unknown> | undefined;
   if (metadata && Object.keys(metadata).length > 0) {
     lines.push('');
@@ -84,6 +112,19 @@ function formatInstanceDetail(instance: Record<string, unknown>, inspect?: Recor
     }
   }
 
+  // Events section (k8s-style)
+  const events = instance.events as Array<{ timestamp: string; type: string; message: string }> | undefined;
+  if (events && events.length > 0) {
+    lines.push('');
+    lines.push('Events:');
+    const tsW = 26;
+    const typeW = 10;
+    lines.push(`  ${'TIMESTAMP'.padEnd(tsW)}${'TYPE'.padEnd(typeW)}MESSAGE`);
+    for (const ev of events) {
+      lines.push(`  ${(ev.timestamp ?? '').padEnd(tsW)}${(ev.type ?? '').padEnd(typeW)}${ev.message ?? ''}`);
+    }
+  }
+
   lines.push('');
   lines.push(`  ${pad('ID:', 12)}${instance.id}`);
   if (instance.createdAt) lines.push(`  ${pad('Created:', 12)}${instance.createdAt}`);
@@ -92,36 +133,6 @@ function formatInstanceDetail(instance: Record<string, unknown>, inspect?: Recor
   return lines.join('\n');
 }
 
-function formatProfileDetail(profile: Record<string, unknown>): string {
-  const lines: string[] = [];
-  lines.push(`=== Profile: ${profile.name} ===`);
-  lines.push(`${pad('Name:')}${profile.name}`);
-  lines.push(`${pad('Server ID:')}${profile.serverId}`);
-
-  const permissions = profile.permissions as string[] | undefined;
-  if (permissions && permissions.length > 0) {
-    lines.push(`${pad('Permissions:')}${permissions.join(', ')}`);
-  }
-
-  const envOverrides = profile.envOverrides as Record<string, string> | undefined;
-  if (envOverrides && Object.keys(envOverrides).length > 0) {
-    lines.push('');
-    lines.push('Environment Overrides:');
-    const keyW = Math.max(4, ...Object.keys(envOverrides).map((k) => k.length)) + 2;
-    for (const [key, value] of Object.entries(envOverrides)) {
-      lines.push(`  ${key.padEnd(keyW)}${value}`);
-    }
-  }
-
-  lines.push('');
-  lines.push('Metadata:');
-  lines.push(`  ${pad('ID:', 12)}${profile.id}`);
-  if (profile.createdAt) lines.push(`  ${pad('Created:', 12)}${profile.createdAt}`);
-  if (profile.updatedAt) lines.push(`  ${pad('Updated:', 12)}${profile.updatedAt}`);
-
-  return lines.join('\n');
-}
-
 function formatProjectDetail(project: Record<string, unknown>): string {
   const lines: string[] = [];
   lines.push(`=== Project: ${project.name} ===`);
@@ -138,6 +149,97 @@ function formatProjectDetail(project: Record<string, unknown>): string {
   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 formatTemplateDetail(template: Record<string, unknown>): string {
+  const lines: string[] = [];
+  lines.push(`=== Template: ${template.name} ===`);
+  lines.push(`${pad('Name:')}${template.name}`);
+  lines.push(`${pad('Version:')}${template.version ?? '1.0.0'}`);
+  lines.push(`${pad('Transport:')}${template.transport ?? 'STDIO'}`);
+  lines.push(`${pad('Replicas:')}${template.replicas ?? 1}`);
+  if (template.dockerImage) lines.push(`${pad('Docker Image:')}${template.dockerImage}`);
+  if (template.packageName) lines.push(`${pad('Package:')}${template.packageName}`);
+  if (template.externalUrl) lines.push(`${pad('External URL:')}${template.externalUrl}`);
+  if (template.repositoryUrl) lines.push(`${pad('Repository:')}${template.repositoryUrl}`);
+  if (template.containerPort) lines.push(`${pad('Container Port:')}${template.containerPort}`);
+  if (template.description) lines.push(`${pad('Description:')}${template.description}`);
+
+  const command = template.command as string[] | null;
+  if (command && command.length > 0) {
+    lines.push('');
+    lines.push('Command:');
+    lines.push(`  ${command.join(' ')}`);
+  }
+
+  const env = template.env as Array<{ name: string; description?: string; required?: boolean; defaultValue?: string }> | undefined;
+  if (env && env.length > 0) {
+    lines.push('');
+    lines.push('Environment Variables:');
+    const nameW = Math.max(6, ...env.map((e) => e.name.length)) + 2;
+    lines.push(`  ${'NAME'.padEnd(nameW)}${'REQUIRED'.padEnd(10)}DESCRIPTION`);
+    for (const e of env) {
+      const req = e.required ? 'yes' : 'no';
+      const desc = e.description ?? '';
+      lines.push(`  ${e.name.padEnd(nameW)}${req.padEnd(10)}${desc}`);
+    }
+  }
+
+  const hc = template.healthCheck as { tool: string; arguments?: Record<string, unknown>; intervalSeconds?: number; timeoutSeconds?: number; failureThreshold?: number } | null;
+  if (hc) {
+    lines.push('');
+    lines.push('Health Check:');
+    lines.push(`  ${pad('Tool:', 22)}${hc.tool}`);
+    if (hc.arguments && Object.keys(hc.arguments).length > 0) {
+      lines.push(`  ${pad('Arguments:', 22)}${JSON.stringify(hc.arguments)}`);
+    }
+    lines.push(`  ${pad('Interval:', 22)}${hc.intervalSeconds ?? 60}s`);
+    lines.push(`  ${pad('Timeout:', 22)}${hc.timeoutSeconds ?? 10}s`);
+    lines.push(`  ${pad('Failure Threshold:', 22)}${hc.failureThreshold ?? 3}`);
+  }
+
+  lines.push('');
+  lines.push('Usage:');
+  lines.push(`  mcpctl create server my-${template.name} --from-template=${template.name}`);
+
+  lines.push('');
+  lines.push('Metadata:');
+  lines.push(`  ${pad('ID:', 12)}${template.id}`);
+  if (template.createdAt) lines.push(`  ${pad('Created:', 12)}${template.createdAt}`);
+  if (template.updatedAt) lines.push(`  ${pad('Updated:', 12)}${template.updatedAt}`);
+
+  return lines.join('\n');
+}
+
 function formatGenericDetail(obj: Record<string, unknown>): string {
   const lines: string[] = [];
   for (const [key, value] of Object.entries(obj)) {
@@ -167,19 +269,42 @@ function formatGenericDetail(obj: Record<string, unknown>): string {
 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('<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, idOrName: 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);
 
       // Resolve name → ID
       let id: string;
+      if (resource === 'instances') {
+        // Instances: accept instance ID or server name (resolve to first running instance)
+        try {
+          id = await resolveNameOrId(deps.client, resource, idOrName);
+        } catch {
+          // Not an instance ID — try as server name
+          const servers = await deps.client.get<Array<{ id: string; name: string }>>('/api/v1/servers');
+          const server = servers.find((s) => s.name === idOrName || s.id === idOrName);
+          if (server) {
+            const instances = await deps.client.get<Array<{ id: string; status: string }>>(`/api/v1/instances?serverId=${server.id}`);
+            const running = instances.find((i) => i.status === 'RUNNING') ?? instances[0];
+            if (running) {
+              id = running.id;
+            } else {
+              throw new Error(`No instances found for server '${idOrName}'`);
+            }
+          } else {
+            id = idOrName;
+          }
+        }
+      } else {
         try {
           id = await resolveNameOrId(deps.client, resource, idOrName);
         } catch {
           id = idOrName;
         }
+      }
 
       const item = await deps.fetchResource(resource, id) as Record<string, unknown>;
 
@@ -207,8 +332,11 @@ export function createDescribeCommand(deps: DescribeCommandDeps): Command {
           case 'instances':
             deps.log(formatInstanceDetail(item, inspect));
             break;
-          case 'profiles':
-            deps.log(formatProfileDetail(item));
+          case 'secrets':
+            deps.log(formatSecretDetail(item, opts.showValues === true));
+            break;
+          case 'templates':
+            deps.log(formatTemplateDetail(item));
             break;
           case 'projects':
             deps.log(formatProjectDetail(item));

src/cli/src/commands/edit.ts

@@ -33,8 +33,8 @@ export function createEditCommand(deps: EditCommandDeps): Command {
   const { client, log } = deps;
 
   return new Command('edit')
-    .description('Edit a resource in your default editor (server, profile, project)')
-    .argument('<resource>', 'Resource type (server, profile, project)')
+    .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);
@@ -47,7 +47,7 @@ export function createEditCommand(deps: EditCommandDeps): Command {
         return;
       }
 
-      const validResources = ['servers', 'profiles', 'projects'];
+      const validResources = ['servers', 'secrets', 'projects'];
       if (!validResources.includes(resource)) {
         log(`Error: unknown resource type '${resourceArg}'`);
         process.exitCode = 1;

src/cli/src/commands/get.ts

@@ -17,12 +17,6 @@ interface ServerRow {
   dockerImage: string | null;
 }
 
-interface ProfileRow {
-  id: string;
-  name: string;
-  serverId: string;
-}
-
 interface ProjectRow {
   id: string;
   name: string;
@@ -30,12 +24,29 @@ interface ProjectRow {
   ownerId: string;
 }
 
+interface SecretRow {
+  id: string;
+  name: string;
+  data: Record<string, string>;
+}
+
+interface TemplateRow {
+  id: string;
+  name: string;
+  version: string;
+  transport: string;
+  packageName: string | null;
+  description: string;
+}
+
 interface InstanceRow {
   id: string;
   serverId: string;
+  server?: { name: string };
   status: string;
   containerId: string | null;
   port: number | null;
+  healthStatus: string | null;
 }
 
 const serverColumns: Column<ServerRow>[] = [
@@ -46,12 +57,6 @@ 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 },
@@ -59,9 +64,24 @@ 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 templateColumns: Column<TemplateRow>[] = [
+  { header: 'NAME', key: 'name' },
+  { header: 'VERSION', key: 'version', width: 10 },
+  { header: 'TRANSPORT', key: 'transport', width: 16 },
+  { header: 'PACKAGE', key: (r) => r.packageName ?? '-' },
+  { header: 'DESCRIPTION', key: 'description', width: 50 },
+];
+
 const instanceColumns: Column<InstanceRow>[] = [
+  { header: 'NAME', key: (r) => r.server?.name ?? '-', width: 20 },
   { header: 'STATUS', key: 'status', width: 10 },
-  { header: 'SERVER ID', key: 'serverId' },
+  { header: 'HEALTH', key: (r) => r.healthStatus ?? '-', width: 10 },
   { header: 'PORT', key: (r) => r.port != null ? String(r.port) : '-', width: 6 },
   { header: 'CONTAINER', key: (r) => r.containerId ? r.containerId.slice(0, 12) : '-', width: 14 },
   { header: 'ID', key: 'id' },
@@ -71,10 +91,12 @@ 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 'templates':
+      return templateColumns as unknown as Column<Record<string, unknown>>[];
     case 'instances':
       return instanceColumns as unknown as Column<Record<string, unknown>>[];
     default:
@@ -91,21 +113,15 @@ function getColumnsForResource(resource: string): Column<Record<string, unknown>
  */
 function toApplyFormat(resource: string, items: unknown[]): Record<string, unknown[]> {
   const cleaned = items.map((item) => {
-    const obj = stripInternalFields(item as Record<string, unknown>);
-    // For profiles: convert serverId → server (name) for apply compat
-    // We can't resolve the name here without an API call, so keep serverId
-    // but also remove it's not in the apply schema. Actually profiles use
-    // "server" (name) in apply format but serverId from API. Keep serverId
-    // since it can still be used with apply (the apply command resolves names).
-    return obj;
+    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)')
+    .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 }) => {

src/cli/src/commands/logs.ts

@@ -6,15 +6,84 @@ export interface LogsCommandDeps {
   log: (...args: unknown[]) => void;
 }
 
+interface InstanceInfo {
+  id: string;
+  status: string;
+  containerId: string | null;
+}
+
+/**
+ * Resolve a name/ID to an instance ID.
+ * Accepts: instance ID, server name, or server ID.
+ * For servers with multiple replicas, picks by --instance index or first RUNNING.
+ */
+async function resolveInstance(
+  client: ApiClient,
+  nameOrId: string,
+  instanceIndex?: number,
+): Promise<{ instanceId: string; serverName?: string; replicaInfo?: string }> {
+  // Try as instance ID first
+  try {
+    await client.get(`/api/v1/instances/${nameOrId}`);
+    return { instanceId: nameOrId };
+  } catch {
+    // Not a valid instance ID
+  }
+
+  // Try as server name/ID → find its instances
+  const servers = await client.get<Array<{ id: string; name: string }>>('/api/v1/servers');
+  const server = servers.find((s) => s.name === nameOrId || s.id === nameOrId);
+  if (!server) {
+    throw new Error(`Instance or server '${nameOrId}' not found`);
+  }
+
+  const instances = await client.get<InstanceInfo[]>(`/api/v1/instances?serverId=${server.id}`);
+  if (instances.length === 0) {
+    throw new Error(`No instances found for server '${server.name}'`);
+  }
+
+  // Select by index or pick first running
+  let selected: InstanceInfo | undefined;
+  if (instanceIndex !== undefined) {
+    if (instanceIndex < 0 || instanceIndex >= instances.length) {
+      throw new Error(`Instance index ${instanceIndex} out of range (server '${server.name}' has ${instances.length} instance${instances.length > 1 ? 's' : ''})`);
+    }
+    selected = instances[instanceIndex];
+  } else {
+    selected = instances.find((i) => i.status === 'RUNNING') ?? instances[0];
+  }
+
+  if (!selected) {
+    throw new Error(`No instances found for server '${server.name}'`);
+  }
+
+  const result: { instanceId: string; serverName?: string; replicaInfo?: string } = {
+    instanceId: selected.id,
+    serverName: server.name,
+  };
+  if (instances.length > 1) {
+    result.replicaInfo = `instance ${instances.indexOf(selected) + 1}/${instances.length}`;
+  }
+  return result;
+}
+
 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')
+    .argument('<name>', 'Server name, server ID, or 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`;
+    .option('-i, --instance <index>', 'Instance/replica index (0-based, for servers with multiple replicas)')
+    .action(async (nameOrId: string, opts: { tail?: string; instance?: string }) => {
+      const instanceIndex = opts.instance !== undefined ? parseInt(opts.instance, 10) : undefined;
+      const { instanceId, serverName, replicaInfo } = await resolveInstance(client, nameOrId, instanceIndex);
+
+      if (replicaInfo) {
+        process.stderr.write(`Showing logs for ${serverName} (${replicaInfo})\n`);
+      }
+
+      let url = `/api/v1/instances/${instanceId}/logs`;
       if (opts.tail) {
         url += `?tail=${opts.tail}`;
       }

src/cli/src/commands/project.ts

@@ -1,60 +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;
-
+export function createProjectCommand(_deps: ProjectCommandDeps): Command {
   const cmd = new Command('project')
     .alias('proj')
     .description('Project-specific actions (create with "create project", list with "get projects")');
 
-  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}'.`);
-    });
-
   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

@@ -3,12 +3,14 @@ import type { ApiClient } from '../api-client.js';
 export const RESOURCE_ALIASES: Record<string, string> = {
   server: 'servers',
   srv: 'servers',
-  profile: 'profiles',
-  prof: 'profiles',
   project: 'projects',
   proj: 'projects',
   instance: 'instances',
   inst: 'instances',
+  secret: 'secrets',
+  sec: 'secrets',
+  template: 'templates',
+  tpl: 'templates',
 };
 
 export function resolveResource(name: string): string {

src/cli/src/index.ts

@@ -10,12 +10,11 @@ import { createLogsCommand } from './commands/logs.js';
 import { createApplyCommand } from './commands/apply.js';
 import { createCreateCommand } from './commands/create.js';
 import { createEditCommand } from './commands/edit.js';
-import { createSetupCommand } from './commands/setup.js';
 import { createClaudeCommand } from './commands/claude.js';
 import { createProjectCommand } from './commands/project.js';
 import { createBackupCommand, createRestoreCommand } from './commands/backup.js';
 import { createLoginCommand, createLogoutCommand } from './commands/auth.js';
-import { ApiClient } from './api-client.js';
+import { ApiClient, ApiError } from './api-client.js';
 import { loadConfig } from './config/index.js';
 import { loadCredentials } from './auth/index.js';
 import { resolveNameOrId } from './commands/shared.js';
@@ -25,7 +24,7 @@ export function createProgram(): 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');
 
@@ -51,6 +50,10 @@ export function createProgram(): Command {
 
   const fetchResource = async (resource: string, nameOrId?: string): Promise<unknown[]> => {
     if (nameOrId) {
+      // Glob pattern — use query param filtering
+      if (nameOrId.includes('*')) {
+        return client.get<unknown[]>(`/api/v1/${resource}?name=${encodeURIComponent(nameOrId)}`);
+      }
       let id: string;
       try {
         id = await resolveNameOrId(client, resource, nameOrId);
@@ -110,33 +113,6 @@ 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),
@@ -167,5 +143,21 @@ const isDirectRun =
   import.meta.url === `file://${process.argv[1]}`;
 
 if (isDirectRun) {
-  createProgram().parseAsync(process.argv);
+  createProgram().parseAsync(process.argv).catch((err: unknown) => {
+    if (err instanceof ApiError) {
+      let msg: string;
+      try {
+        const parsed = JSON.parse(err.body) as { error?: string; message?: string };
+        msg = parsed.error ?? parsed.message ?? err.body;
+      } catch {
+        msg = err.body;
+      }
+      console.error(`Error: ${msg}`);
+    } else if (err instanceof Error) {
+      console.error(`Error: ${err.message}`);
+    } else {
+      console.error(`Error: ${String(err)}`);
+    }
+    process.exit(1);
+  });
 }

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

@@ -1,6 +1,6 @@
 import { describe, it, expect, vi, beforeEach } from 'vitest';
 import { createCreateCommand } from '../../src/commands/create.js';
-import type { ApiClient } from '../../src/api-client.js';
+import { type ApiClient, ApiError } from '../../src/api-client.js';
 
 function mockClient(): ApiClient {
   return {
@@ -46,8 +46,8 @@ describe('create command', () => {
         '--command', 'python',
         '--command', '-c',
         '--command', 'print("hello")',
-        '--env-template', 'API_KEY:API key:true',
-        '--env-template', 'BASE_URL:Base URL:false',
+        '--env', 'API_KEY=secretRef:creds:API_KEY',
+        '--env', 'BASE_URL=http://localhost',
       ], { from: 'user' });
 
       expect(client.post).toHaveBeenCalledWith('/api/v1/servers', {
@@ -59,9 +59,9 @@ describe('create command', () => {
         containerPort: 3000,
         replicas: 2,
         command: ['python', '-c', 'print("hello")'],
-        envTemplate: [
-          { name: 'API_KEY', description: 'API key', isSecret: true },
-          { name: 'BASE_URL', description: 'Base URL', isSecret: false },
+        env: [
+          { name: 'API_KEY', valueFrom: { secretRef: { name: 'creds', key: 'API_KEY' } } },
+          { name: 'BASE_URL', value: 'http://localhost' },
         ],
       });
     });
@@ -73,51 +73,98 @@ describe('create command', () => {
         transport: 'STDIO',
       }));
     });
-  });
 
-  describe('create profile', () => {
-    it('creates a profile resolving server name', async () => {
-      vi.mocked(client.get).mockResolvedValue([
-        { id: 'srv-abc', name: 'ha-mcp' },
-      ]);
-      const cmd = createCreateCommand({ client, log });
-      await cmd.parseAsync(['profile', 'production', '--server', 'ha-mcp'], { from: 'user' });
-      expect(client.post).toHaveBeenCalledWith('/api/v1/profiles', expect.objectContaining({
-        name: 'production',
-        serverId: 'srv-abc',
-      }));
-    });
-
-    it('parses --env KEY=value entries', async () => {
-      vi.mocked(client.get).mockResolvedValue([
-        { id: 'srv-1', name: 'test' },
-      ]);
+    it('strips null values from template when using --from-template', async () => {
+      vi.mocked(client.get).mockResolvedValueOnce([{
+        id: 'tpl-1',
+        name: 'grafana',
+        version: '1.0.0',
+        description: 'Grafana MCP',
+        packageName: '@leval/mcp-grafana',
+        dockerImage: null,
+        transport: 'STDIO',
+        repositoryUrl: 'https://github.com/test',
+        externalUrl: null,
+        command: null,
+        containerPort: null,
+        replicas: 1,
+        env: [{ name: 'TOKEN', required: true, description: 'A token' }],
+        healthCheck: { tool: 'test', arguments: {} },
+        createdAt: '2025-01-01',
+        updatedAt: '2025-01-01',
+      }] as never);
       const cmd = createCreateCommand({ client, log });
       await cmd.parseAsync([
-        'profile', 'dev',
-        '--server', 'test',
-        '--env', 'FOO=bar',
-        '--env', 'SECRET=s3cr3t',
+        'server', 'my-grafana', '--from-template=grafana',
+        '--env', 'TOKEN=secretRef:creds:TOKEN',
       ], { from: 'user' });
-      expect(client.post).toHaveBeenCalledWith('/api/v1/profiles', expect.objectContaining({
-        envOverrides: { FOO: 'bar', SECRET: 's3cr3t' },
-      }));
+      const call = vi.mocked(client.post).mock.calls[0]![1] as Record<string, unknown>;
+      // null fields from template should NOT be in the body
+      expect(call).not.toHaveProperty('dockerImage');
+      expect(call).not.toHaveProperty('externalUrl');
+      expect(call).not.toHaveProperty('command');
+      expect(call).not.toHaveProperty('containerPort');
+      // non-null fields should be present
+      expect(call.packageName).toBe('@leval/mcp-grafana');
+      expect(call.healthCheck).toEqual({ tool: 'test', arguments: {} });
+      expect(call.templateName).toBe('grafana');
     });
 
-    it('passes permissions', async () => {
-      vi.mocked(client.get).mockResolvedValue([
-        { id: 'srv-1', name: 'test' },
-      ]);
+    it('throws on 409 without --force', async () => {
+      vi.mocked(client.post).mockRejectedValueOnce(new ApiError(409, '{"error":"Server already exists: my-server"}'));
+      const cmd = createCreateCommand({ client, log });
+      await expect(cmd.parseAsync(['server', 'my-server'], { from: 'user' })).rejects.toThrow('API error 409');
+    });
+
+    it('updates existing server on 409 with --force', async () => {
+      vi.mocked(client.post).mockRejectedValueOnce(new ApiError(409, '{"error":"Server already exists"}'));
+      vi.mocked(client.get).mockResolvedValueOnce([{ id: 'srv-1', name: 'my-server' }] as never);
+      const cmd = createCreateCommand({ client, log });
+      await cmd.parseAsync(['server', 'my-server', '--force'], { from: 'user' });
+      expect(client.put).toHaveBeenCalledWith('/api/v1/servers/srv-1', expect.objectContaining({
+        transport: 'STDIO',
+      }));
+      expect(output.join('\n')).toContain("server 'my-server' updated");
+    });
+  });
+
+  describe('create secret', () => {
+    it('creates a secret with --data flags', async () => {
       const cmd = createCreateCommand({ client, log });
       await cmd.parseAsync([
-        'profile', 'admin',
-        '--server', 'test',
-        '--permissions', 'read',
-        '--permissions', 'write',
+        'secret', 'ha-creds',
+        '--data', 'TOKEN=abc123',
+        '--data', 'URL=https://ha.local',
       ], { from: 'user' });
-      expect(client.post).toHaveBeenCalledWith('/api/v1/profiles', expect.objectContaining({
-        permissions: ['read', 'write'],
-      }));
+      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: {},
+      });
+    });
+
+    it('throws on 409 without --force', async () => {
+      vi.mocked(client.post).mockRejectedValueOnce(new ApiError(409, '{"error":"Secret already exists: my-creds"}'));
+      const cmd = createCreateCommand({ client, log });
+      await expect(cmd.parseAsync(['secret', 'my-creds', '--data', 'KEY=val'], { from: 'user' })).rejects.toThrow('API error 409');
+    });
+
+    it('updates existing secret on 409 with --force', async () => {
+      vi.mocked(client.post).mockRejectedValueOnce(new ApiError(409, '{"error":"Secret already exists"}'));
+      vi.mocked(client.get).mockResolvedValueOnce([{ id: 'sec-1', name: 'my-creds' }] as never);
+      const cmd = createCreateCommand({ client, log });
+      await cmd.parseAsync(['secret', 'my-creds', '--data', 'KEY=val', '--force'], { from: 'user' });
+      expect(client.put).toHaveBeenCalledWith('/api/v1/secrets/sec-1', { data: { KEY: 'val' } });
+      expect(output.join('\n')).toContain("secret 'my-creds' updated");
     });
   });
 
@@ -140,5 +187,14 @@ describe('create command', () => {
         description: '',
       });
     });
+
+    it('updates existing project on 409 with --force', async () => {
+      vi.mocked(client.post).mockRejectedValueOnce(new ApiError(409, '{"error":"Project already exists"}'));
+      vi.mocked(client.get).mockResolvedValueOnce([{ id: 'proj-1', name: 'my-proj' }] as never);
+      const cmd = createCreateCommand({ client, log });
+      await cmd.parseAsync(['project', 'my-proj', '-d', 'updated', '--force'], { from: 'user' });
+      expect(client.put).toHaveBeenCalledWith('/api/v1/projects/proj-1', { description: 'updated' });
+      expect(output.join('\n')).toContain("project 'my-proj' updated");
+    });
   });
 });

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

@@ -30,7 +30,7 @@ describe('describe command', () => {
       transport: 'STDIO',
       packageName: '@slack/mcp',
       dockerImage: null,
-      envTemplate: [],
+      env: [],
       createdAt: '2025-01-01',
     });
     const cmd = createDescribeCommand(deps);
@@ -50,10 +50,10 @@ describe('describe command', () => {
   });
 
   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 () => {
@@ -72,26 +72,6 @@ describe('describe command', () => {
     expect(deps.output[0]).toContain('name: slack');
   });
 
-  it('shows profile with permissions and env overrides', async () => {
-    const deps = makeDeps({
-      id: 'p1',
-      name: 'production',
-      serverId: 'srv-1',
-      permissions: ['read', 'write'],
-      envOverrides: { FOO: 'bar', SECRET: 's3cr3t' },
-      createdAt: '2025-01-01',
-    });
-    const cmd = createDescribeCommand(deps);
-    await cmd.parseAsync(['node', 'test', 'profile', 'p1']);
-
-    const text = deps.output.join('\n');
-    expect(text).toContain('=== Profile: production ===');
-    expect(text).toContain('read, write');
-    expect(text).toContain('Environment Overrides:');
-    expect(text).toContain('FOO');
-    expect(text).toContain('bar');
-  });
-
   it('shows project detail', async () => {
     const deps = makeDeps({
       id: 'proj-1',
@@ -109,6 +89,39 @@ describe('describe command', () => {
     expect(text).toContain('user-1');
   });
 
+  it('shows secret detail with masked values', async () => {
+    const deps = makeDeps({
+      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', 'secret', 'sec-1']);
+
+    const text = deps.output.join('\n');
+    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',
@@ -126,4 +139,152 @@ describe('describe command', () => {
     expect(text).toContain('RUNNING');
     expect(text).toContain('abc123');
   });
+
+  it('resolves server name to instance for describe instance', async () => {
+    const deps = makeDeps({
+      id: 'inst-1',
+      serverId: 'srv-1',
+      server: { name: 'my-grafana' },
+      status: 'RUNNING',
+      containerId: 'abc123',
+      port: 3000,
+    });
+    // resolveNameOrId will throw (not a CUID, name won't match instances)
+    vi.mocked(deps.client.get)
+      .mockResolvedValueOnce([] as never) // instances list (no name match)
+      .mockResolvedValueOnce([{ id: 'srv-1', name: 'my-grafana' }] as never) // servers list
+      .mockResolvedValueOnce([{ id: 'inst-1', status: 'RUNNING' }] as never); // instances for server
+
+    const cmd = createDescribeCommand(deps);
+    await cmd.parseAsync(['node', 'test', 'instance', 'my-grafana']);
+
+    expect(deps.fetchResource).toHaveBeenCalledWith('instances', 'inst-1');
+  });
+
+  it('resolves server name and picks running instance over stopped', async () => {
+    const deps = makeDeps({
+      id: 'inst-2',
+      serverId: 'srv-1',
+      server: { name: 'my-ha' },
+      status: 'RUNNING',
+      containerId: 'def456',
+    });
+    vi.mocked(deps.client.get)
+      .mockResolvedValueOnce([] as never) // instances list
+      .mockResolvedValueOnce([{ id: 'srv-1', name: 'my-ha' }] as never)
+      .mockResolvedValueOnce([
+        { id: 'inst-1', status: 'ERROR' },
+        { id: 'inst-2', status: 'RUNNING' },
+      ] as never);
+
+    const cmd = createDescribeCommand(deps);
+    await cmd.parseAsync(['node', 'test', 'instance', 'my-ha']);
+
+    expect(deps.fetchResource).toHaveBeenCalledWith('instances', 'inst-2');
+  });
+
+  it('throws when no instances found for server name', async () => {
+    const deps = makeDeps();
+    vi.mocked(deps.client.get)
+      .mockResolvedValueOnce([] as never) // instances list
+      .mockResolvedValueOnce([{ id: 'srv-1', name: 'my-server' }] as never)
+      .mockResolvedValueOnce([] as never); // no instances
+
+    const cmd = createDescribeCommand(deps);
+    await expect(cmd.parseAsync(['node', 'test', 'instance', 'my-server'])).rejects.toThrow(
+      /No instances found/,
+    );
+  });
+
+  it('shows instance with server name in header', async () => {
+    const deps = makeDeps({
+      id: 'inst-1',
+      serverId: 'srv-1',
+      server: { name: 'my-grafana' },
+      status: 'RUNNING',
+      containerId: 'abc123',
+      port: 3000,
+    });
+    const cmd = createDescribeCommand(deps);
+    await cmd.parseAsync(['node', 'test', 'instance', 'inst-1']);
+
+    const text = deps.output.join('\n');
+    expect(text).toContain('=== Instance: my-grafana ===');
+  });
+
+  it('shows instance health and events', async () => {
+    const deps = makeDeps({
+      id: 'inst-1',
+      serverId: 'srv-1',
+      server: { name: 'my-grafana' },
+      status: 'RUNNING',
+      containerId: 'abc123',
+      healthStatus: 'healthy',
+      lastHealthCheck: '2025-01-15T10:30:00Z',
+      events: [
+        { timestamp: '2025-01-15T10:30:00Z', type: 'Normal', message: 'Health check passed (45ms)' },
+      ],
+    });
+    const cmd = createDescribeCommand(deps);
+    await cmd.parseAsync(['node', 'test', 'instance', 'inst-1']);
+
+    const text = deps.output.join('\n');
+    expect(text).toContain('Health:');
+    expect(text).toContain('healthy');
+    expect(text).toContain('Events:');
+    expect(text).toContain('Health check passed');
+  });
+
+  it('shows server healthCheck section', async () => {
+    const deps = makeDeps({
+      id: 'srv-1',
+      name: 'my-grafana',
+      transport: 'STDIO',
+      healthCheck: {
+        tool: 'list_datasources',
+        arguments: {},
+        intervalSeconds: 60,
+        timeoutSeconds: 10,
+        failureThreshold: 3,
+      },
+    });
+    const cmd = createDescribeCommand(deps);
+    await cmd.parseAsync(['node', 'test', 'server', 'srv-1']);
+
+    const text = deps.output.join('\n');
+    expect(text).toContain('Health Check:');
+    expect(text).toContain('list_datasources');
+    expect(text).toContain('60s');
+    expect(text).toContain('Failure Threshold:');
+  });
+
+  it('shows template detail with healthCheck and usage', async () => {
+    const deps = makeDeps({
+      id: 'tpl-1',
+      name: 'grafana',
+      transport: 'STDIO',
+      version: '1.0.0',
+      packageName: '@leval/mcp-grafana',
+      env: [
+        { name: 'GRAFANA_URL', required: true, description: 'Grafana instance URL' },
+      ],
+      healthCheck: {
+        tool: 'list_datasources',
+        arguments: {},
+        intervalSeconds: 60,
+        timeoutSeconds: 10,
+        failureThreshold: 3,
+      },
+    });
+    const cmd = createDescribeCommand(deps);
+    await cmd.parseAsync(['node', 'test', 'template', 'tpl-1']);
+
+    const text = deps.output.join('\n');
+    expect(text).toContain('=== Template: grafana ===');
+    expect(text).toContain('@leval/mcp-grafana');
+    expect(text).toContain('GRAFANA_URL');
+    expect(text).toContain('Health Check:');
+    expect(text).toContain('list_datasources');
+    expect(text).toContain('mcpctl create server my-grafana --from-template=grafana');
+  });
 });

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

@@ -150,31 +150,4 @@ describe('edit command', () => {
     expect(output.join('\n')).toContain('immutable');
   });
 
-  it('edits a profile', async () => {
-    vi.mocked(client.get).mockImplementation(async (path: string) => {
-      if (path === '/api/v1/profiles') return [{ id: 'prof-1', name: 'production' }];
-      return {
-        id: 'prof-1', name: 'production', serverId: 'srv-1',
-        permissions: ['read'], envOverrides: { FOO: 'bar' },
-        createdAt: '2025-01-01', updatedAt: '2025-01-01', version: 1,
-      };
-    });
-
-    const cmd = createEditCommand({
-      client,
-      log,
-      getEditor: () => 'vi',
-      openEditor: (filePath) => {
-        const content = readFileSync(filePath, 'utf-8');
-        const modified = content.replace('FOO: bar', 'FOO: baz');
-        writeFileSync(filePath, modified, 'utf-8');
-      },
-    });
-
-    await cmd.parseAsync(['profile', 'production'], { from: 'user' });
-
-    expect(client.put).toHaveBeenCalledWith('/api/v1/profiles/prof-1', expect.objectContaining({
-      envOverrides: { FOO: 'baz' },
-    }));
-  });
 });

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

@@ -67,23 +67,15 @@ describe('get command', () => {
     expect(text).not.toContain('createdAt:');
   });
 
-  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');
-  });
-
   it('lists instances with correct columns', async () => {
     const deps = makeDeps([
-      { id: 'inst-1', serverId: 'srv-1', status: 'RUNNING', containerId: 'abc123def456', port: 3000 },
+      { id: 'inst-1', serverId: 'srv-1', server: { name: 'my-grafana' }, status: 'RUNNING', containerId: 'abc123def456', port: 3000 },
     ]);
     const cmd = createGetCommand(deps);
     await cmd.parseAsync(['node', 'test', 'instances']);
+    expect(deps.output[0]).toContain('NAME');
     expect(deps.output[0]).toContain('STATUS');
+    expect(deps.output.join('\n')).toContain('my-grafana');
     expect(deps.output.join('\n')).toContain('RUNNING');
   });
 

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

@@ -45,12 +45,6 @@ describe('delete command', () => {
     expect(client.delete).toHaveBeenCalledWith('/api/v1/servers/srv-abc');
   });
 
-  it('deletes a profile', async () => {
-    const cmd = createDeleteCommand({ client, log });
-    await cmd.parseAsync(['profile', 'prof-1'], { from: 'user' });
-    expect(client.delete).toHaveBeenCalledWith('/api/v1/profiles/prof-1');
-  });
-
   it('deletes a project', async () => {
     const cmd = createDeleteCommand({ client, log });
     await cmd.parseAsync(['project', 'proj-1'], { from: 'user' });
@@ -74,16 +68,79 @@ describe('logs command', () => {
     output = [];
   });
 
-  it('shows logs', async () => {
-    vi.mocked(client.get).mockResolvedValue({ stdout: 'hello world\n', stderr: '' });
+  it('shows logs by instance ID', async () => {
+    vi.mocked(client.get)
+      .mockResolvedValueOnce({ id: 'inst-1', status: 'RUNNING' } as never) // instance lookup
+      .mockResolvedValueOnce({ stdout: 'hello world\n', stderr: '' } as never); // logs
     const cmd = createLogsCommand({ client, log });
     await cmd.parseAsync(['inst-1'], { from: 'user' });
+    expect(client.get).toHaveBeenCalledWith('/api/v1/instances/inst-1');
     expect(client.get).toHaveBeenCalledWith('/api/v1/instances/inst-1/logs');
     expect(output.join('\n')).toContain('hello world');
   });
 
+  it('resolves server name to instance ID', async () => {
+    vi.mocked(client.get)
+      .mockRejectedValueOnce(new Error('not found')) // instance lookup fails
+      .mockResolvedValueOnce([{ id: 'srv-1', name: 'my-grafana' }] as never) // servers list
+      .mockResolvedValueOnce([{ id: 'inst-1', status: 'RUNNING', containerId: 'abc' }] as never) // instances for server
+      .mockResolvedValueOnce({ stdout: 'grafana logs\n', stderr: '' } as never); // logs
+    const cmd = createLogsCommand({ client, log });
+    await cmd.parseAsync(['my-grafana'], { from: 'user' });
+    expect(client.get).toHaveBeenCalledWith('/api/v1/instances/inst-1/logs');
+    expect(output.join('\n')).toContain('grafana logs');
+  });
+
+  it('picks RUNNING instance over others', async () => {
+    vi.mocked(client.get)
+      .mockRejectedValueOnce(new Error('not found'))
+      .mockResolvedValueOnce([{ id: 'srv-1', name: 'ha-mcp' }] as never)
+      .mockResolvedValueOnce([
+        { id: 'inst-err', status: 'ERROR', containerId: null },
+        { id: 'inst-ok', status: 'RUNNING', containerId: 'abc' },
+      ] as never)
+      .mockResolvedValueOnce({ stdout: 'running instance\n', stderr: '' } as never);
+    const cmd = createLogsCommand({ client, log });
+    await cmd.parseAsync(['ha-mcp'], { from: 'user' });
+    expect(client.get).toHaveBeenCalledWith('/api/v1/instances/inst-ok/logs');
+  });
+
+  it('selects specific replica with --instance', async () => {
+    vi.mocked(client.get)
+      .mockRejectedValueOnce(new Error('not found'))
+      .mockResolvedValueOnce([{ id: 'srv-1', name: 'ha-mcp' }] as never)
+      .mockResolvedValueOnce([
+        { id: 'inst-0', status: 'RUNNING', containerId: 'a' },
+        { id: 'inst-1', status: 'RUNNING', containerId: 'b' },
+      ] as never)
+      .mockResolvedValueOnce({ stdout: 'replica 1\n', stderr: '' } as never);
+    const cmd = createLogsCommand({ client, log });
+    await cmd.parseAsync(['ha-mcp', '-i', '1'], { from: 'user' });
+    expect(client.get).toHaveBeenCalledWith('/api/v1/instances/inst-1/logs');
+  });
+
+  it('throws on out-of-range --instance index', async () => {
+    vi.mocked(client.get)
+      .mockRejectedValueOnce(new Error('not found'))
+      .mockResolvedValueOnce([{ id: 'srv-1', name: 'ha-mcp' }] as never)
+      .mockResolvedValueOnce([{ id: 'inst-0', status: 'RUNNING' }] as never);
+    const cmd = createLogsCommand({ client, log });
+    await expect(cmd.parseAsync(['ha-mcp', '-i', '5'], { from: 'user' })).rejects.toThrow('out of range');
+  });
+
+  it('throws when server has no instances', async () => {
+    vi.mocked(client.get)
+      .mockRejectedValueOnce(new Error('not found'))
+      .mockResolvedValueOnce([{ id: 'srv-1', name: 'empty-srv' }] as never)
+      .mockResolvedValueOnce([] as never);
+    const cmd = createLogsCommand({ client, log });
+    await expect(cmd.parseAsync(['empty-srv'], { from: 'user' })).rejects.toThrow('No instances found');
+  });
+
   it('passes tail option', async () => {
-    vi.mocked(client.get).mockResolvedValue({ stdout: '', stderr: '' });
+    vi.mocked(client.get)
+      .mockResolvedValueOnce({ id: 'inst-1' } as never)
+      .mockResolvedValueOnce({ stdout: '', stderr: '' } as never);
     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

@@ -21,32 +21,9 @@ describe('project command', () => {
     output = [];
   });
 
-  describe('profiles', () => {
-    it('lists profiles for a project', async () => {
-      vi.mocked(client.get).mockResolvedValue([
-        { id: 'prof-1', name: 'default', serverId: 'srv-1' },
-      ]);
+  it('creates command with alias', () => {
     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)');
-    });
+    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

@@ -21,7 +21,6 @@ describe('CLI command registration (e2e)', () => {
     expect(commandNames).toContain('apply');
     expect(commandNames).toContain('create');
     expect(commandNames).toContain('edit');
-    expect(commandNames).toContain('setup');
     expect(commandNames).toContain('claude');
     expect(commandNames).toContain('project');
     expect(commandNames).toContain('backup');
@@ -46,19 +45,11 @@ describe('CLI command registration (e2e)', () => {
     expect(subcommands).toContain('remove');
   });
 
-  it('project command has action subcommands only', () => {
+  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('profiles');
-    expect(subcommands).toContain('set-profiles');
-    // create is now top-level (mcpctl create project)
-    expect(subcommands).not.toContain('create');
-    expect(subcommands).not.toContain('list');
-    expect(subcommands).not.toContain('show');
-    expect(subcommands).not.toContain('delete');
+    expect(project!.alias()).toBe('proj');
   });
 
   it('displays version', () => {

src/db/prisma/schema.prisma

@@ -61,12 +61,15 @@ model McpServer {
   command       Json?
   containerPort Int?
   replicas      Int             @default(1)
-  envTemplate   Json            @default("[]")
+  env           Json            @default("[]")
+  healthCheck   Json?
   version       Int             @default(1)
   createdAt     DateTime        @default(now())
   updatedAt     DateTime        @updatedAt
 
-  profiles  McpProfile[]
+  templateName    String?
+  templateVersion String?
+
   instances McpInstance[]
 
   @@index([name])
@@ -78,23 +81,40 @@ enum Transport {
   STREAMABLE_HTTP
 }
 
-// ── MCP Profiles ──
+// ── MCP Templates ──
 
-model McpProfile {
+model McpTemplate {
   id            String    @id @default(cuid())
-  name        String
-  serverId    String
-  permissions Json     @default("[]")
-  envOverrides Json    @default("{}")
+  name          String    @unique
+  version       String    @default("1.0.0")
+  description   String    @default("")
+  packageName   String?
+  dockerImage   String?
+  transport     Transport @default(STDIO)
+  repositoryUrl String?
+  externalUrl   String?
+  command       Json?
+  containerPort Int?
+  replicas      Int       @default(1)
+  env           Json      @default("[]")
+  healthCheck   Json?
+  createdAt     DateTime  @default(now())
+  updatedAt     DateTime  @updatedAt
+
+  @@index([name])
+}
+
+// ── Secrets ──
+
+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 ──
@@ -109,27 +129,11 @@ 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 {
@@ -139,6 +143,9 @@ model McpInstance {
   status      InstanceStatus @default(STOPPED)
   port        Int?
   metadata        Json           @default("{}")
+  healthStatus    String?
+  lastHealthCheck DateTime?
+  events          Json           @default("[]")
   version         Int            @default(1)
   createdAt       DateTime       @default(now())
   updatedAt       DateTime       @updatedAt

src/db/src/index.ts

@@ -4,9 +4,9 @@ export type {
   User,
   Session,
   McpServer,
-  McpProfile,
+  McpTemplate,
+  Secret,
   Project,
-  ProjectMcpProfile,
   McpInstance,
   AuditLog,
   Role,
@@ -14,5 +14,5 @@ export type {
   InstanceStatus,
 } from '@prisma/client';
 
-export { seedMcpServers, defaultServers } from './seed/index.js';
-export type { SeedServer } from './seed/index.js';
+export { seedTemplates } from './seed/index.js';
+export type { SeedTemplate, TemplateEnvEntry, HealthCheckSpec } from './seed/index.js';

src/db/src/seed/index.ts

@@ -1,131 +1,77 @@
-import { PrismaClient } from '@prisma/client';
+import { PrismaClient, Prisma } from '@prisma/client';
 
-export interface SeedServer {
+export interface TemplateEnvEntry {
   name: string;
-  description: string;
-  packageName: string;
-  transport: 'STDIO' | 'SSE' | 'STREAMABLE_HTTP';
-  repositoryUrl: string;
-  envTemplate: Array<{
-    name: string;
-    description: string;
-    isSecret: boolean;
-    setupUrl?: string;
-  }>;
+  description?: string;
+  required?: boolean;
+  defaultValue?: string;
 }
 
-export const defaultServers: SeedServer[] = [
-  {
-    name: 'slack',
-    description: 'Slack MCP server for reading channels, messages, and user info',
-    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,
-      },
-    ],
-  },
-  {
-    name: 'jira',
-    description: 'Jira MCP server for issues, projects, and boards',
-    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',
-      },
-    ],
-  },
-  {
-    name: 'github',
-    description: 'GitHub MCP server for repos, issues, PRs, and code search',
-    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',
-      },
-    ],
-  },
-  {
-    name: 'terraform',
-    description: 'Terraform MCP server for infrastructure documentation and state',
-    packageName: '@anthropic/terraform-mcp',
-    transport: 'STDIO',
-    repositoryUrl: 'https://github.com/modelcontextprotocol/servers/tree/main/src/terraform',
-    envTemplate: [],
-  },
-];
+export interface HealthCheckSpec {
+  tool: string;
+  arguments?: Record<string, unknown>;
+  intervalSeconds?: number;
+  timeoutSeconds?: number;
+  failureThreshold?: number;
+}
 
-export async function seedMcpServers(
+export interface SeedTemplate {
+  name: string;
+  version: string;
+  description: string;
+  packageName?: string;
+  dockerImage?: string;
+  transport: 'STDIO' | 'SSE' | 'STREAMABLE_HTTP';
+  repositoryUrl?: string;
+  externalUrl?: string;
+  command?: string[];
+  containerPort?: number;
+  replicas?: number;
+  env?: TemplateEnvEntry[];
+  healthCheck?: HealthCheckSpec;
+}
+
+export async function seedTemplates(
   prisma: PrismaClient,
-  servers: SeedServer[] = defaultServers,
+  templates: SeedTemplate[],
 ): Promise<number> {
-  let created = 0;
+  let upserted = 0;
 
-  for (const server of servers) {
-    await prisma.mcpServer.upsert({
-      where: { name: server.name },
+  for (const tpl of templates) {
+    await prisma.mcpTemplate.upsert({
+      where: { name: tpl.name },
       update: {
-        description: server.description,
-        packageName: server.packageName,
-        transport: server.transport,
-        repositoryUrl: server.repositoryUrl,
-        envTemplate: server.envTemplate,
+        version: tpl.version,
+        description: tpl.description,
+        packageName: tpl.packageName ?? null,
+        dockerImage: tpl.dockerImage ?? null,
+        transport: tpl.transport,
+        repositoryUrl: tpl.repositoryUrl ?? null,
+        externalUrl: tpl.externalUrl ?? null,
+        command: (tpl.command ?? Prisma.JsonNull) as Prisma.InputJsonValue,
+        containerPort: tpl.containerPort ?? null,
+        replicas: tpl.replicas ?? 1,
+        env: (tpl.env ?? []) as unknown as Prisma.InputJsonValue,
+        healthCheck: (tpl.healthCheck ?? Prisma.JsonNull) as unknown as Prisma.InputJsonValue,
       },
       create: {
-        name: server.name,
-        description: server.description,
-        packageName: server.packageName,
-        transport: server.transport,
-        repositoryUrl: server.repositoryUrl,
-        envTemplate: server.envTemplate,
+        name: tpl.name,
+        version: tpl.version,
+        description: tpl.description,
+        packageName: tpl.packageName ?? null,
+        dockerImage: tpl.dockerImage ?? null,
+        transport: tpl.transport,
+        repositoryUrl: tpl.repositoryUrl ?? null,
+        externalUrl: tpl.externalUrl ?? null,
+        command: (tpl.command ?? Prisma.JsonNull) as Prisma.InputJsonValue,
+        containerPort: tpl.containerPort ?? null,
+        replicas: tpl.replicas ?? 1,
+        env: (tpl.env ?? []) as unknown as Prisma.InputJsonValue,
+        healthCheck: (tpl.healthCheck ?? Prisma.JsonNull) as unknown as Prisma.InputJsonValue,
       },
     });
-    created++;
+    upserted++;
   }
 
-  return created;
-}
-
-// CLI entry point
-if (import.meta.url === `file://${process.argv[1]}`) {
-  const prisma = new PrismaClient();
-  seedMcpServers(prisma)
-    .then((count) => {
-      console.log(`Seeded ${count} MCP servers`);
-      return prisma.$disconnect();
-    })
-    .catch((e) => {
-      console.error(e);
-      return prisma.$disconnect().then(() => process.exit(1));
-    });
+  return upserted;
 }

src/db/tests/helpers.ts

@@ -48,11 +48,11 @@ 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();
+  await client.mcpTemplate.deleteMany();
   await client.user.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('updates data', async () => {
+    const secret = await prisma.secret.create({
+      data: { name: 'updatable', data: { KEY: 'old' } },
     });
-
-  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);
+    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

@@ -1,7 +1,8 @@
 import { describe, it, expect, beforeAll, afterAll, beforeEach } from 'vitest';
 import type { PrismaClient } from '@prisma/client';
 import { setupTestDb, cleanupTestDb, clearAllTables } from './helpers.js';
-import { seedMcpServers, defaultServers } from '../src/seed/index.js';
+import { seedTemplates } from '../src/seed/index.js';
+import type { SeedTemplate } from '../src/seed/index.js';
 
 let prisma: PrismaClient;
 
@@ -17,55 +18,69 @@ beforeEach(async () => {
   await clearAllTables(prisma);
 });
 
-describe('seedMcpServers', () => {
-  it('seeds all default servers', async () => {
-    const count = await seedMcpServers(prisma);
-    expect(count).toBe(defaultServers.length);
+const testTemplates: SeedTemplate[] = [
+  {
+    name: 'github',
+    version: '1.0.0',
+    description: 'GitHub MCP server',
+    packageName: '@anthropic/github-mcp',
+    transport: 'STDIO',
+    env: [{ name: 'GITHUB_TOKEN', description: 'Personal access token', required: true }],
+  },
+  {
+    name: 'slack',
+    version: '1.0.0',
+    description: 'Slack MCP server',
+    packageName: '@anthropic/slack-mcp',
+    transport: 'STDIO',
+    env: [],
+  },
+];
 
-    const servers = await prisma.mcpServer.findMany({ orderBy: { name: 'asc' } });
-    expect(servers).toHaveLength(defaultServers.length);
+describe('seedTemplates', () => {
+  it('seeds templates', async () => {
+    const count = await seedTemplates(prisma, testTemplates);
+    expect(count).toBe(2);
 
-    const names = servers.map((s) => s.name);
-    expect(names).toContain('slack');
-    expect(names).toContain('github');
-    expect(names).toContain('jira');
-    expect(names).toContain('terraform');
+    const templates = await prisma.mcpTemplate.findMany({ orderBy: { name: 'asc' } });
+    expect(templates).toHaveLength(2);
+    expect(templates.map((t) => t.name)).toEqual(['github', 'slack']);
   });
 
   it('is idempotent (upsert)', async () => {
-    await seedMcpServers(prisma);
-    const count = await seedMcpServers(prisma);
-    expect(count).toBe(defaultServers.length);
+    await seedTemplates(prisma, testTemplates);
+    const count = await seedTemplates(prisma, testTemplates);
+    expect(count).toBe(2);
 
-    const servers = await prisma.mcpServer.findMany();
-    expect(servers).toHaveLength(defaultServers.length);
+    const templates = await prisma.mcpTemplate.findMany();
+    expect(templates).toHaveLength(2);
   });
 
-  it('seeds envTemplate 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);
+  it('seeds env correctly', async () => {
+    await seedTemplates(prisma, testTemplates);
+    const github = await prisma.mcpTemplate.findUnique({ where: { name: 'github' } });
+    const env = github!.env as Array<{ name: string; description?: string; required?: boolean }>;
+    expect(env).toHaveLength(1);
+    expect(env[0].name).toBe('GITHUB_TOKEN');
+    expect(env[0].required).toBe(true);
   });
 
-  it('accepts custom server list', async () => {
-    const custom = [
+  it('accepts custom template list', async () => {
+    const custom: SeedTemplate[] = [
       {
-        name: 'custom-server',
-        description: 'Custom test server',
+        name: 'custom-template',
+        version: '2.0.0',
+        description: 'Custom test template',
         packageName: '@test/custom',
-        transport: 'STDIO' as const,
-        repositoryUrl: 'https://example.com',
-        envTemplate: [],
+        transport: 'STDIO',
+        env: [],
       },
     ];
-    const count = await seedMcpServers(prisma, custom);
+    const count = await seedTemplates(prisma, custom);
     expect(count).toBe(1);
 
-    const servers = await prisma.mcpServer.findMany();
-    expect(servers).toHaveLength(1);
-    expect(servers[0].name).toBe('custom-server');
+    const templates = await prisma.mcpTemplate.findMany();
+    expect(templates).toHaveLength(1);
+    expect(templates[0].name).toBe('custom-template');
   });
 });

src/mcpd/package.json

@@ -23,11 +23,13 @@
     "bcrypt": "^5.1.1",
     "dockerode": "^4.0.9",
     "fastify": "^5.0.0",
+    "js-yaml": "^4.1.0",
     "zod": "^3.24.0"
   },
   "devDependencies": {
     "@types/bcrypt": "^5.0.2",
     "@types/dockerode": "^4.0.1",
+    "@types/js-yaml": "^4.0.9",
     "@types/node": "^25.3.0"
   }
 }

src/mcpd/src/main.ts

@@ -1,18 +1,23 @@
+import { readdirSync, readFileSync } from 'node:fs';
+import { join } from 'node:path';
 import { PrismaClient } from '@prisma/client';
-import { seedMcpServers } from '@mcpctl/db';
+import yaml from 'js-yaml';
+import { seedTemplates } from '@mcpctl/db';
+import type { SeedTemplate } from '@mcpctl/db';
 import { loadConfigFromEnv } from './config/index.js';
 import { createServer } from './server.js';
 import { setupGracefulShutdown } from './utils/index.js';
 import {
   McpServerRepository,
-  McpProfileRepository,
+  SecretRepository,
   McpInstanceRepository,
   ProjectRepository,
   AuditLogRepository,
+  TemplateRepository,
 } from './repositories/index.js';
 import {
   McpServerService,
-  McpProfileService,
+  SecretService,
   InstanceService,
   ProjectService,
   AuditLogService,
@@ -23,10 +28,11 @@ import {
   RestoreService,
   AuthService,
   McpProxyService,
+  TemplateService,
 } from './services/index.js';
 import {
   registerMcpServerRoutes,
-  registerMcpProfileRoutes,
+  registerSecretRoutes,
   registerInstanceRoutes,
   registerProjectRoutes,
   registerAuditLogRoutes,
@@ -34,6 +40,7 @@ import {
   registerBackupRoutes,
   registerAuthRoutes,
   registerMcpProxyRoutes,
+  registerTemplateRoutes,
 } from './routes/index.js';
 
 async function main(): Promise<void> {
@@ -45,31 +52,52 @@ async function main(): Promise<void> {
   });
   await prisma.$connect();
 
-  // Seed default servers (upsert, safe to repeat)
-  await seedMcpServers(prisma);
+  // Seed templates from YAML files
+  const templatesDir = process.env.TEMPLATES_DIR ?? 'templates';
+  const templateFiles = (() => {
+    try {
+      return readdirSync(templatesDir).filter((f) => f.endsWith('.yaml') || f.endsWith('.yml'));
+    } catch {
+      return [];
+    }
+  })();
+  const templates: SeedTemplate[] = templateFiles.map((f) => {
+    const content = readFileSync(join(templatesDir, f), 'utf-8');
+    const parsed = yaml.load(content) as SeedTemplate;
+    return {
+      ...parsed,
+      transport: parsed.transport ?? 'STDIO',
+      version: parsed.version ?? '1.0.0',
+      description: parsed.description ?? '',
+      ...(parsed.healthCheck ? { healthCheck: parsed.healthCheck } : {}),
+    };
+  });
+  await seedTemplates(prisma, templates);
 
   // 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);
+  const templateRepo = new TemplateRepository(prisma);
 
   // Orchestrator
   const orchestrator = new DockerContainerManager();
 
   // Services
   const serverService = new McpServerService(serverRepo);
-  const instanceService = new InstanceService(instanceRepo, serverRepo, orchestrator);
+  const instanceService = new InstanceService(instanceRepo, serverRepo, orchestrator, secretRepo);
   serverService.setInstanceService(instanceService);
-  const profileService = new McpProfileService(profileRepo, serverRepo);
-  const projectService = new ProjectService(projectRepo, profileRepo, serverRepo);
+  const secretService = new SecretService(secretRepo);
+  const projectService = new ProjectService(projectRepo);
   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 templateService = new TemplateService(templateRepo);
   const mcpProxyService = new McpProxyService(instanceRepo, serverRepo);
 
   // Server
@@ -88,7 +116,8 @@ async function main(): Promise<void> {
 
   // Routes
   registerMcpServerRoutes(app, serverService, instanceService);
-  registerMcpProfileRoutes(app, profileService);
+  registerTemplateRoutes(app, templateService);
+  registerSecretRoutes(app, secretService);
   registerInstanceRoutes(app, instanceService);
   registerProjectRoutes(app, projectService);
   registerAuditLogRoutes(app, auditLogService);
@@ -105,9 +134,22 @@ async function main(): Promise<void> {
   await app.listen({ port: config.port, host: config.host });
   app.log.info(`mcpd listening on ${config.host}:${config.port}`);
 
+  // Periodic container liveness sync — detect crashed containers
+  const SYNC_INTERVAL_MS = 30_000; // 30s
+  const syncTimer = setInterval(async () => {
+    try {
+      await instanceService.syncStatus();
+    } catch (err) {
+      app.log.error({ err }, 'Container status sync failed');
+    }
+  }, SYNC_INTERVAL_MS);
+
   // Graceful shutdown
   setupGracefulShutdown(app, {
-    disconnectDb: () => prisma.$disconnect(),
+    disconnectDb: async () => {
+      clearInterval(syncTimer);
+      await prisma.$disconnect();
+    },
   });
 }
 

src/mcpd/src/repositories/index.ts

@@ -1,7 +1,9 @@
-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';
 export { AuditLogRepository } from './audit-log.repository.js';
+export type { ITemplateRepository } from './template.repository.js';
+export { TemplateRepository } from './template.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[]>;
@@ -16,16 +16,16 @@ export interface IMcpInstanceRepository {
   findById(id: string): Promise<McpInstance | null>;
   findByContainerId(containerId: string): Promise<McpInstance | null>;
   create(data: { serverId: string; containerId?: string; status?: InstanceStatus; port?: number; metadata?: Record<string, unknown> }): Promise<McpInstance>;
-  updateStatus(id: string, status: InstanceStatus, fields?: { containerId?: string; port?: number; metadata?: Record<string, unknown> }): Promise<McpInstance>;
+  updateStatus(id: string, status: InstanceStatus, fields?: { containerId?: string; port?: number; metadata?: Record<string, unknown>; healthStatus?: string; lastHealthCheck?: Date; events?: unknown[] }): Promise<McpInstance>;
   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-instance.repository.ts

@@ -11,6 +11,7 @@ export class McpInstanceRepository implements IMcpInstanceRepository {
     }
     return this.prisma.mcpInstance.findMany({
       where,
+      include: { server: { select: { name: true } } },
       orderBy: { createdAt: 'desc' },
     });
   }
@@ -44,7 +45,7 @@ export class McpInstanceRepository implements IMcpInstanceRepository {
   async updateStatus(
     id: string,
     status: InstanceStatus,
-    fields?: { containerId?: string; port?: number; metadata?: Record<string, unknown> },
+    fields?: { containerId?: string; port?: number; metadata?: Record<string, unknown>; healthStatus?: string; lastHealthCheck?: Date; events?: unknown[] },
   ): Promise<McpInstance> {
     const updateData: Prisma.McpInstanceUpdateInput = {
       status,
@@ -59,6 +60,15 @@ export class McpInstanceRepository implements IMcpInstanceRepository {
     if (fields?.metadata !== undefined) {
       updateData.metadata = fields.metadata as Prisma.InputJsonValue;
     }
+    if (fields?.healthStatus !== undefined) {
+      updateData.healthStatus = fields.healthStatus;
+    }
+    if (fields?.lastHealthCheck !== undefined) {
+      updateData.lastHealthCheck = fields.lastHealthCheck;
+    }
+    if (fields?.events !== undefined) {
+      updateData.events = fields.events as unknown as Prisma.InputJsonValue;
+    }
     return this.prisma.mcpInstance.update({
       where: { id },
       data: updateData,

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

@@ -30,7 +30,8 @@ export class McpServerRepository implements IMcpServerRepository {
         command: data.command ?? Prisma.DbNull,
         containerPort: data.containerPort ?? null,
         replicas: data.replicas,
-        envTemplate: data.envTemplate,
+        env: data.env,
+        healthCheck: (data.healthCheck ?? Prisma.JsonNull) as Prisma.InputJsonValue,
       },
     });
   }
@@ -46,7 +47,8 @@ export class McpServerRepository implements IMcpServerRepository {
     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.envTemplate !== undefined) updateData['envTemplate'] = data.envTemplate;
+    if (data.env !== undefined) updateData['env'] = data.env;
+    if (data.healthCheck !== undefined) updateData['healthCheck'] = (data.healthCheck ?? Prisma.JsonNull) as Prisma.InputJsonValue;
 
     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/repositories/template.repository.ts

@@ -0,0 +1,82 @@
+import { type PrismaClient, type McpTemplate, Prisma } from '@prisma/client';
+import type { CreateTemplateInput, UpdateTemplateInput } from '../validation/template.schema.js';
+
+export interface ITemplateRepository {
+  findAll(): Promise<McpTemplate[]>;
+  findById(id: string): Promise<McpTemplate | null>;
+  findByName(name: string): Promise<McpTemplate | null>;
+  search(pattern: string): Promise<McpTemplate[]>;
+  create(data: CreateTemplateInput): Promise<McpTemplate>;
+  update(id: string, data: UpdateTemplateInput): Promise<McpTemplate>;
+  delete(id: string): Promise<void>;
+}
+
+export class TemplateRepository implements ITemplateRepository {
+  constructor(private readonly prisma: PrismaClient) {}
+
+  async findAll(): Promise<McpTemplate[]> {
+    return this.prisma.mcpTemplate.findMany({ orderBy: { name: 'asc' } });
+  }
+
+  async findById(id: string): Promise<McpTemplate | null> {
+    return this.prisma.mcpTemplate.findUnique({ where: { id } });
+  }
+
+  async findByName(name: string): Promise<McpTemplate | null> {
+    return this.prisma.mcpTemplate.findUnique({ where: { name } });
+  }
+
+  async search(pattern: string): Promise<McpTemplate[]> {
+    // Convert glob * to SQL %
+    const sqlPattern = pattern.replace(/\*/g, '%');
+    return this.prisma.mcpTemplate.findMany({
+      where: { name: { contains: sqlPattern.replace(/%/g, ''), mode: 'insensitive' } },
+      orderBy: { name: 'asc' },
+    });
+  }
+
+  async create(data: CreateTemplateInput): Promise<McpTemplate> {
+    return this.prisma.mcpTemplate.create({
+      data: {
+        name: data.name,
+        version: data.version,
+        description: data.description,
+        packageName: data.packageName ?? null,
+        dockerImage: data.dockerImage ?? null,
+        transport: data.transport,
+        repositoryUrl: data.repositoryUrl ?? null,
+        externalUrl: data.externalUrl ?? null,
+        command: (data.command ?? Prisma.JsonNull) as Prisma.InputJsonValue,
+        containerPort: data.containerPort ?? null,
+        replicas: data.replicas,
+        env: (data.env ?? []) as unknown as Prisma.InputJsonValue,
+        healthCheck: (data.healthCheck ?? Prisma.JsonNull) as Prisma.InputJsonValue,
+      },
+    });
+  }
+
+  async update(id: string, data: UpdateTemplateInput): Promise<McpTemplate> {
+    const updateData: Record<string, unknown> = {};
+    if (data.version !== undefined) updateData.version = data.version;
+    if (data.description !== undefined) updateData.description = data.description;
+    if (data.packageName !== undefined) updateData.packageName = data.packageName;
+    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.externalUrl !== undefined) updateData.externalUrl = data.externalUrl;
+    if (data.command !== undefined) updateData.command = (data.command ?? Prisma.JsonNull) as Prisma.InputJsonValue;
+    if (data.containerPort !== undefined) updateData.containerPort = data.containerPort;
+    if (data.replicas !== undefined) updateData.replicas = data.replicas;
+    if (data.env !== undefined) updateData.env = (data.env ?? []) as Prisma.InputJsonValue;
+    if (data.healthCheck !== undefined) updateData.healthCheck = (data.healthCheck ?? Prisma.JsonNull) as Prisma.InputJsonValue;
+
+    return this.prisma.mcpTemplate.update({
+      where: { id },
+      data: updateData,
+    });
+  }
+
+  async delete(id: string): Promise<void> {
+    await this.prisma.mcpTemplate.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';
@@ -13,3 +13,4 @@ export { registerAuthRoutes } from './auth.js';
 export type { AuthRouteDeps } from './auth.js';
 export { registerMcpProxyRoutes } from './mcp-proxy.js';
 export type { McpProxyRouteDeps } from './mcp-proxy.js';
+export { registerTemplateRoutes } from './templates.js';

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/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/routes/templates.ts

@@ -0,0 +1,31 @@
+import type { FastifyInstance } from 'fastify';
+import type { TemplateService } from '../services/template.service.js';
+
+export function registerTemplateRoutes(
+  app: FastifyInstance,
+  service: TemplateService,
+): void {
+  app.get<{ Querystring: { name?: string } }>('/api/v1/templates', async (request) => {
+    const namePattern = request.query.name;
+    return service.list(namePattern);
+  });
+
+  app.get<{ Params: { id: string } }>('/api/v1/templates/:id', async (request) => {
+    return service.getById(request.params.id);
+  });
+
+  app.post('/api/v1/templates', async (request, reply) => {
+    const template = await service.create(request.body);
+    reply.code(201);
+    return template;
+  });
+
+  app.put<{ Params: { id: string } }>('/api/v1/templates/:id', async (request) => {
+    return service.update(request.params.id, request.body);
+  });
+
+  app.delete<{ Params: { id: string } }>('/api/v1/templates/:id', async (request, reply) => {
+    await service.delete(request.params.id);
+    reply.code(204);
+  });
+}

src/mcpd/src/seed-runner.ts

@@ -1,11 +1,45 @@
+import { readdirSync, readFileSync } from 'node:fs';
+import { join } from 'node:path';
 import { PrismaClient } from '@prisma/client';
-import { seedMcpServers } from '@mcpctl/db';
+import yaml from 'js-yaml';
+import { seedTemplates } from '@mcpctl/db';
+import type { SeedTemplate } from '@mcpctl/db';
+
+function loadTemplatesFromDir(dir: string): SeedTemplate[] {
+  let files: string[];
+  try {
+    files = readdirSync(dir).filter((f) => f.endsWith('.yaml') || f.endsWith('.yml'));
+  } catch {
+    console.warn(`Templates directory not found: ${dir}`);
+    return [];
+  }
+
+  const templates: SeedTemplate[] = [];
+  for (const file of files) {
+    const content = readFileSync(join(dir, file), 'utf-8');
+    const parsed = yaml.load(content) as SeedTemplate;
+    if (parsed?.name) {
+      templates.push({
+        ...parsed,
+        transport: parsed.transport ?? 'STDIO',
+        version: parsed.version ?? '1.0.0',
+        description: parsed.description ?? '',
+        ...(parsed.healthCheck ? { healthCheck: parsed.healthCheck } : {}),
+      });
+    }
+  }
+
+  return templates;
+}
 
 async function run(): Promise<void> {
   const prisma = new PrismaClient();
   try {
-    const count = await seedMcpServers(prisma);
-    console.log(`Seeded ${count} MCP servers`);
+    // Look for templates in common locations
+    const templatesDir = process.env.TEMPLATES_DIR ?? 'templates';
+    const templates = loadTemplatesFromDir(templatesDir);
+    const count = await seedTemplates(prisma, templates);
+    console.log(`Seeded ${count} templates from ${templatesDir}`);
   } finally {
     await prisma.$disconnect();
   }

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 {
+      projects = allProjects.map((proj) => ({
         name: proj.name,
         description: proj.description,
-            profileNames: profileIds.map((id) => profileMap.get(id) ?? id),
-          };
-        }),
-      );
+      }));
     }
 
     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 (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 = `profile:${profile.name}:${key}`;
-              secrets[secretKey] = value;
-              (overrides as Record<string, string>)[key] = `__ENCRYPTED:${secretKey}__`;
-            }
+            const secretKey = `secret:${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)) {
+    // 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 = secrets[secretKey];
+          const decrypted = decryptedSecrets[secretKey];
           if (decrypted !== undefined) {
-              overrides[key] = decrypted;
-            }
+            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;
         }
@@ -115,66 +109,44 @@ export class RestoreService {
           description: server.description,
           transport: server.transport as 'STDIO' | 'SSE' | 'STREAMABLE_HTTP',
           replicas: (server as { replicas?: number }).replicas ?? 1,
-          envTemplate: (server.envTemplate ?? []) as Array<{ name: string; description: string; isSecret: boolean }>,
+          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);
+        await this.serverRepo.create(createData);
         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)}`);
       }
     }
 
@@ -191,29 +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

@@ -5,7 +5,7 @@ import type {
   ContainerInfo,
   ContainerLogs,
 } from '../orchestrator.js';
-import { DEFAULT_MEMORY_LIMIT, DEFAULT_NANO_CPUS } from '../orchestrator.js';
+import { DEFAULT_MEMORY_LIMIT } from '../orchestrator.js';
 
 const MCPCTL_LABEL = 'mcpctl.managed';
 
@@ -54,7 +54,7 @@ export class DockerContainerManager implements McpOrchestrator {
 
   async createContainer(spec: ContainerSpec): Promise<ContainerInfo> {
     const memoryLimit = spec.memoryLimit ?? DEFAULT_MEMORY_LIMIT;
-    const nanoCpus = spec.nanoCpus ?? DEFAULT_NANO_CPUS;
+    const nanoCpus = spec.nanoCpus;
 
     const portBindings: Record<string, Array<{ HostPort: string }>> = {};
     const exposedPorts: Record<string, Record<string, never>> = {};
@@ -80,10 +80,13 @@ export class DockerContainerManager implements McpOrchestrator {
       Env: envArr,
       ExposedPorts: exposedPorts,
       Labels: labels,
+      // Keep stdin open for STDIO MCP servers (they read from stdin)
+      OpenStdin: true,
+      StdinOnce: false,
       HostConfig: {
         PortBindings: portBindings,
         Memory: memoryLimit,
-        NanoCpus: nanoCpus,
+        ...(nanoCpus ? { NanoCpus: nanoCpus } : {}),
         NetworkMode: spec.network ?? 'bridge',
       },
     };

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';
@@ -23,3 +24,4 @@ export { AuthService, AuthenticationError } from './auth.service.js';
 export type { LoginResult } from './auth.service.js';
 export { McpProxyService } from './mcp-proxy-service.js';
 export type { McpProxyRequest, McpProxyResponse } from './mcp-proxy-service.js';
+export { TemplateService } from './template.service.js';

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

@@ -1,7 +1,14 @@
 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';
+
+/** Default image for npm-based MCP servers (STDIO with packageName, no dockerImage). */
+const DEFAULT_NODE_RUNNER_IMAGE = process.env['MCPD_NODE_RUNNER_IMAGE'] ?? 'mysources.co.uk/michal/mcpctl-node-runner:latest';
+
+/** Network for MCP server containers (matches docker-compose mcp-servers network). */
+const MCP_SERVERS_NETWORK = process.env['MCPD_MCP_NETWORK'] ?? 'mcp-servers';
 
 export class InvalidStateError extends Error {
   readonly statusCode = 409;
@@ -16,6 +23,7 @@ export class InstanceService {
     private instanceRepo: IMcpInstanceRepository,
     private serverRepo: IMcpServerRepository,
     private orchestrator: McpOrchestrator,
+    private secretRepo?: ISecretRepository,
   ) {}
 
   async list(serverId?: string): Promise<McpInstance[]> {
@@ -28,8 +36,41 @@ export class InstanceService {
     return instance;
   }
 
+  /**
+   * Sync instance statuses with actual container state.
+   * Detects crashed/stopped containers and marks them ERROR.
+   */
+  async syncStatus(): Promise<void> {
+    const instances = await this.instanceRepo.findAll();
+    for (const inst of instances) {
+      if ((inst.status === 'RUNNING' || inst.status === 'STARTING') && inst.containerId) {
+        try {
+          const info = await this.orchestrator.inspectContainer(inst.containerId);
+          if (info.state === 'stopped' || info.state === 'error') {
+            // Container died — get last logs for error context
+            let errorMsg = `Container ${info.state}`;
+            try {
+              const logs = await this.orchestrator.getContainerLogs(inst.containerId, { tail: 5 });
+              const lastLog = (logs.stdout || logs.stderr).trim().split('\n').pop();
+              if (lastLog) errorMsg = lastLog;
+            } catch { /* best-effort */ }
+            await this.instanceRepo.updateStatus(inst.id, 'ERROR', {
+              metadata: { error: errorMsg },
+            });
+          }
+        } catch {
+          // Container gone entirely
+          await this.instanceRepo.updateStatus(inst.id, 'ERROR', {
+            metadata: { error: 'Container not found' },
+          });
+        }
+      }
+    }
+  }
+
   /**
    * Reconcile instances for a server to match desired replica count.
+   * - Syncs container statuses first (detect crashed containers)
    * - If fewer running instances than replicas: start new ones
    * - If more running instances than replicas: remove excess (oldest first)
    */
@@ -37,6 +78,9 @@ export class InstanceService {
     const server = await this.serverRepo.findById(serverId);
     if (!server) throw new NotFoundError(`McpServer '${serverId}' not found`);
 
+    // Sync container statuses before counting active instances
+    await this.syncStatus();
+
     const instances = await this.instanceRepo.findAll(serverId);
     const active = instances.filter((i) => i.status === 'RUNNING' || i.status === 'STARTING');
     const desired = server.replicas;
@@ -137,7 +181,23 @@ export class InstanceService {
       });
     }
 
-    const image = server.dockerImage ?? server.packageName ?? server.name;
+    // Determine image + command based on server config:
+    // 1. Explicit dockerImage → use as-is
+    // 2. packageName (npm) → use node-runner image + npx command
+    // 3. Fallback → server name (legacy)
+    let image: string;
+    let npmCommand: string[] | undefined;
+
+    if (server.dockerImage) {
+      image = server.dockerImage;
+    } else if (server.packageName) {
+      image = DEFAULT_NODE_RUNNER_IMAGE;
+      // Build npx command: entrypoint is ["npx", "-y"], so CMD = [packageName, ...args]
+      const serverCommand = server.command as string[] | null;
+      npmCommand = [server.packageName, ...(serverCommand ?? [])];
+    } else {
+      image = server.name;
+    }
 
     let instance = await this.instanceRepo.create({
       serverId,
@@ -149,6 +209,7 @@ export class InstanceService {
         image,
         name: `mcpctl-${server.name}-${instance.id}`,
         hostPort: null,
+        network: MCP_SERVERS_NETWORK,
         labels: {
           'mcpctl.server-id': serverId,
           'mcpctl.instance-id': instance.id,
@@ -157,10 +218,36 @@ export class InstanceService {
       if (server.transport === 'SSE' || server.transport === 'STREAMABLE_HTTP') {
         spec.containerPort = server.containerPort ?? 3000;
       }
+      // npm-based servers: command = [packageName, ...args] (entrypoint handles npx -y)
+      // Docker-image servers: use explicit command if provided
+      if (npmCommand) {
+        spec.command = npmCommand;
+      } else {
         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
+        }
+      }
+
+      // Pull image if not available locally
+      try {
+        await this.orchestrator.pullImage(image);
+      } catch {
+        // Image may already be available locally
+      }
 
       const containerInfo = await this.orchestrator.createContainer(spec);
 

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/project.service.ts

@@ -1,16 +1,11 @@
 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 { 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,
   ) {}
 
   async list(ownerId?: string): Promise<Project[]> {
@@ -46,41 +41,4 @@ 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/services/template.service.ts

@@ -0,0 +1,53 @@
+import type { McpTemplate } from '@prisma/client';
+import type { ITemplateRepository } from '../repositories/template.repository.js';
+import { CreateTemplateSchema, UpdateTemplateSchema } from '../validation/template.schema.js';
+import { NotFoundError, ConflictError } from './mcp-server.service.js';
+
+export class TemplateService {
+  constructor(private readonly repo: ITemplateRepository) {}
+
+  async list(namePattern?: string): Promise<McpTemplate[]> {
+    if (namePattern) {
+      return this.repo.search(namePattern);
+    }
+    return this.repo.findAll();
+  }
+
+  async getById(id: string): Promise<McpTemplate> {
+    const template = await this.repo.findById(id);
+    if (template === null) {
+      throw new NotFoundError(`Template not found: ${id}`);
+    }
+    return template;
+  }
+
+  async getByName(name: string): Promise<McpTemplate> {
+    const template = await this.repo.findByName(name);
+    if (template === null) {
+      throw new NotFoundError(`Template not found: ${name}`);
+    }
+    return template;
+  }
+
+  async create(input: unknown): Promise<McpTemplate> {
+    const data = CreateTemplateSchema.parse(input);
+
+    const existing = await this.repo.findByName(data.name);
+    if (existing !== null) {
+      throw new ConflictError(`Template already exists: ${data.name}`);
+    }
+
+    return this.repo.create(data);
+  }
+
+  async update(id: string, input: unknown): Promise<McpTemplate> {
+    const data = UpdateTemplateSchema.parse(input);
+    await this.getById(id);
+    return this.repo.update(id, data);
+  }
+
+  async delete(id: string): Promise<void> {
+    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 +1,24 @@
 import { z } from 'zod';
+import { HealthCheckSchema } from './template.schema.js';
 
-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(''),
@@ -18,7 +30,8 @@ export const CreateMcpServerSchema = z.object({
   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),
-  envTemplate: z.array(EnvTemplateEntrySchema).default([]),
+  env: z.array(ServerEnvEntrySchema).default([]),
+  healthCheck: HealthCheckSchema.optional(),
 });
 
 export const UpdateMcpServerSchema = z.object({
@@ -31,7 +44,8 @@ export const UpdateMcpServerSchema = z.object({
   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(),
-  envTemplate: z.array(EnvTemplateEntrySchema).optional(),
+  env: z.array(ServerEnvEntrySchema).optional(),
+  healthCheck: HealthCheckSchema.nullable().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/src/validation/template.schema.ts

@@ -0,0 +1,39 @@
+import { z } from 'zod';
+
+const TemplateEnvEntrySchema = z.object({
+  name: z.string().min(1),
+  description: z.string().optional(),
+  required: z.boolean().optional(),
+  defaultValue: z.string().optional(),
+});
+
+export const HealthCheckSchema = z.object({
+  tool: z.string().min(1),
+  arguments: z.record(z.unknown()).default({}),
+  intervalSeconds: z.number().int().min(5).max(3600).default(60),
+  timeoutSeconds: z.number().int().min(1).max(120).default(10),
+  failureThreshold: z.number().int().min(1).max(20).default(3),
+});
+
+export type HealthCheckInput = z.infer<typeof HealthCheckSchema>;
+
+export const CreateTemplateSchema = z.object({
+  name: z.string().min(1).max(100).regex(/^[a-z0-9-]+$/, 'Name must be lowercase alphanumeric with hyphens'),
+  version: z.string().default('1.0.0'),
+  description: z.string().default(''),
+  packageName: z.string().optional(),
+  dockerImage: z.string().optional(),
+  transport: z.enum(['STDIO', 'SSE', 'STREAMABLE_HTTP']).default('STDIO'),
+  repositoryUrl: z.string().optional(),
+  externalUrl: z.string().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(TemplateEnvEntrySchema).default([]),
+  healthCheck: HealthCheckSchema.optional(),
+});
+
+export const UpdateTemplateSchema = CreateTemplateSchema.partial().omit({ name: true });
+
+export type CreateTemplateInput = z.infer<typeof CreateTemplateSchema>;
+export type UpdateTemplateInput = z.infer<typeof UpdateTemplateSchema>;

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

@@ -83,7 +83,7 @@ function makeServer(overrides: Partial<{ id: string; name: string; replicas: num
     command: overrides.command ?? null,
     containerPort: overrides.containerPort ?? null,
     replicas: overrides.replicas ?? 1,
-    envTemplate: [],
+    env: [],
     version: 1,
     createdAt: new Date(),
     updatedAt: new Date(),

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

@@ -44,7 +44,7 @@ function createInMemoryServerRepo(): IMcpServerRepository {
         command: data.command ?? null,
         containerPort: data.containerPort ?? null,
         replicas: data.replicas ?? 1,
-        envTemplate: data.envTemplate ?? [],
+        env: data.env ?? [],
         version: 1,
         createdAt: new Date(),
         updatedAt: new Date(),
@@ -347,8 +347,8 @@ describe('MCP server full flow', () => {
           transport: 'STREAMABLE_HTTP',
           externalUrl: `http://localhost:${fakeMcpPort}`,
           containerPort: 3000,
-          envTemplate: [
-            { name: 'HOMEASSISTANT_TOKEN', description: 'HA token', isSecret: true },
+          env: [
+            { name: 'HOMEASSISTANT_TOKEN', value: 'placeholder' },
           ],
         },
       });
@@ -463,9 +463,9 @@ describe('MCP server full flow', () => {
           transport: 'STREAMABLE_HTTP',
           containerPort: 3000,
           command: ['python', '-c', 'print("hello")'],
-          envTemplate: [
-            { name: 'HOMEASSISTANT_URL', description: 'HA URL' },
-            { name: 'HOMEASSISTANT_TOKEN', description: 'HA token', isSecret: true },
+          env: [
+            { name: 'HOMEASSISTANT_URL', value: 'http://localhost:8123' },
+            { name: 'HOMEASSISTANT_TOKEN', valueFrom: { secretRef: { name: 'ha-secrets', key: 'token' } } },
           ],
         },
       });

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

@@ -34,7 +34,7 @@ function mockRepo(): IMcpServerRepository {
         command: null,
         containerPort: null,
         replicas: data.replicas ?? 1,
-        envTemplate: [],
+        env: [],
         version: 1,
         createdAt: new Date(),
         updatedAt: new Date(),
@@ -55,7 +55,7 @@ function mockRepo(): IMcpServerRepository {
         command: null,
         containerPort: null,
         replicas: 1,
-        envTemplate: [],
+        env: [],
         version: 2,
         createdAt: new Date(),
         updatedAt: new Date(),

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

@@ -2,8 +2,6 @@ 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';
-
 function mockProjectRepo(): IProjectRepository {
   return {
     findAll: vi.fn(async () => []),
@@ -23,44 +21,16 @@ 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 () => {}),
-  };
-}
-
-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('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);
   });
 
   describe('create', () => {
@@ -86,55 +56,6 @@ 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/mcpd/tsconfig.json

@@ -3,7 +3,7 @@
   "compilerOptions": {
     "rootDir": "src",
     "outDir": "dist",
-    "types": ["node"]
+    "types": ["node", "js-yaml"]
   },
   "include": ["src/**/*.ts"],
   "references": [

src/mcplocal/src/http/index.ts

@@ -4,3 +4,4 @@ export { loadHttpConfig } from './config.js';
 export type { HttpConfig } from './config.js';
 export { McpdClient, AuthenticationError, ConnectionError } from './mcpd-client.js';
 export { registerProxyRoutes } from './routes/proxy.js';
+export { registerMcpEndpoint } from './mcp-endpoint.js';

src/mcplocal/src/http/mcp-endpoint.ts

@@ -0,0 +1,100 @@
+/**
+ * Streamable HTTP MCP protocol endpoint.
+ *
+ * Exposes the McpRouter over HTTP at /mcp so Claude Code can connect
+ * via `{ "type": "http", "url": "http://localhost:3200/mcp" }` in .mcp.json.
+ *
+ * Each client session gets its own StreamableHTTPServerTransport, but all
+ * share the same McpRouter (and therefore the same upstream connections).
+ */
+import { randomUUID } from 'node:crypto';
+import type { FastifyInstance } from 'fastify';
+import { StreamableHTTPServerTransport } from '@modelcontextprotocol/sdk/server/streamableHttp.js';
+import type { JSONRPCMessage } from '@modelcontextprotocol/sdk/types.js';
+import type { McpRouter } from '../router.js';
+import type { JsonRpcRequest } from '../types.js';
+
+interface SessionEntry {
+  transport: StreamableHTTPServerTransport;
+}
+
+export function registerMcpEndpoint(app: FastifyInstance, router: McpRouter): void {
+  const sessions = new Map<string, SessionEntry>();
+
+  // POST /mcp — JSON-RPC requests (initialize, tools/call, etc.)
+  app.post('/mcp', async (request, reply) => {
+    const sessionId = request.headers['mcp-session-id'] as string | undefined;
+
+    if (sessionId && sessions.has(sessionId)) {
+      // Existing session
+      const session = sessions.get(sessionId)!;
+      await session.transport.handleRequest(request.raw, reply.raw, request.body);
+      // Fastify must not send its own response — the transport already did
+      reply.hijack();
+      return;
+    }
+
+    if (sessionId && !sessions.has(sessionId)) {
+      // Unknown session
+      reply.code(404).send({ error: 'Session not found' });
+      return;
+    }
+
+    // New session — no session ID header
+    const transport = new StreamableHTTPServerTransport({
+      sessionIdGenerator: () => randomUUID(),
+      onsessioninitialized: (id) => {
+        sessions.set(id, { transport });
+      },
+    });
+
+    // Wire transport messages to the router
+    transport.onmessage = async (message: JSONRPCMessage) => {
+      // The transport sends us JSON-RPC messages; route them through McpRouter
+      if ('method' in message && 'id' in message) {
+        const response = await router.route(message as unknown as JsonRpcRequest);
+        await transport.send(response as unknown as JSONRPCMessage);
+      }
+      // Notifications (no id) are ignored — router doesn't handle inbound notifications
+    };
+
+    transport.onclose = () => {
+      const id = transport.sessionId;
+      if (id) {
+        sessions.delete(id);
+      }
+    };
+
+    await transport.handleRequest(request.raw, reply.raw, request.body);
+    reply.hijack();
+  });
+
+  // GET /mcp — SSE stream for server-initiated notifications
+  app.get('/mcp', async (request, reply) => {
+    const sessionId = request.headers['mcp-session-id'] as string | undefined;
+
+    if (!sessionId || !sessions.has(sessionId)) {
+      reply.code(400).send({ error: 'Invalid or missing session ID' });
+      return;
+    }
+
+    const session = sessions.get(sessionId)!;
+    await session.transport.handleRequest(request.raw, reply.raw);
+    reply.hijack();
+  });
+
+  // DELETE /mcp — Session cleanup
+  app.delete('/mcp', async (request, reply) => {
+    const sessionId = request.headers['mcp-session-id'] as string | undefined;
+
+    if (!sessionId || !sessions.has(sessionId)) {
+      reply.code(400).send({ error: 'Invalid or missing session ID' });
+      return;
+    }
+
+    const session = sessions.get(sessionId)!;
+    await session.transport.handleRequest(request.raw, reply.raw);
+    sessions.delete(sessionId);
+    reply.hijack();
+  });
+}

src/mcplocal/src/http/server.ts

@@ -5,6 +5,7 @@ import { APP_VERSION } from '@mcpctl/shared';
 import type { HttpConfig } from './config.js';
 import { McpdClient } from './mcpd-client.js';
 import { registerProxyRoutes } from './routes/proxy.js';
+import { registerMcpEndpoint } from './mcp-endpoint.js';
 import type { McpRouter } from '../router.js';
 import type { HealthMonitor } from '../health.js';
 import type { TieredHealthMonitor } from '../health/tiered.js';
@@ -81,5 +82,8 @@ export async function createHttpServer(
   const mcpdClient = new McpdClient(config.mcpdUrl, config.mcpdToken);
   registerProxyRoutes(app, mcpdClient);
 
+  // Streamable HTTP MCP protocol endpoint at /mcp
+  registerMcpEndpoint(app, deps.router);
+
   return app;
 }

src/mcplocal/src/main.ts

@@ -141,7 +141,10 @@ export async function main(argv: string[] = process.argv): Promise<MainResult> {
 }
 
 // Run when executed directly
-const isMain = process.argv[1]?.endsWith('main.js') || process.argv[1]?.endsWith('main.ts');
+const isMain =
+  process.argv[1]?.endsWith('main.js') ||
+  process.argv[1]?.endsWith('main.ts') ||
+  process.argv[1]?.endsWith('mcpctl-local');
 if (isMain) {
   main().catch((err) => {
     process.stderr.write(`Fatal: ${err}\n`);

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',
-};