src/mcplocal/src/discovery.ts

@@ -167,12 +167,16 @@ function syncUpstreams(router: McpRouter, mcpdClient: McpdClient, servers: McpdS
     }
   }
 
-  // Add/update upstreams for each server
+  // Add/update upstreams for each server. Always rebuild, even when an
+  // upstream with this name already exists: McpdUpstream binds the caller's
+  // bearer token (and the server id) at construction, and a cached project
+  // router outlives both. Reusing the old object meant a token rotation left
+  // every pre-rotation server silently 401-ing on tools/list — attached,
+  // healthy, zero tools, no error — while servers attached after the rotation
+  // worked, because only THEY got an upstream carrying the fresh token.
   for (const server of servers) {
-    if (!currentNames.has(server.name)) {
-      const upstream = new McpdUpstream(server.id, server.name, toolClient, server.description, discoveryClient);
-      router.addUpstream(upstream);
-    }
+    const upstream = new McpdUpstream(server.id, server.name, toolClient, server.description, discoveryClient);
+    router.addUpstream(upstream);
     // Applied on every sync, not just on first registration: raising a
     // server's timeout should take effect at the next refresh rather than
     // requiring the upstream to be dropped and rebuilt.

src/mcplocal/src/proxymodel/plugin-context.ts

@@ -19,6 +19,7 @@ export interface PluginContextDeps {
   cache: CacheProvider;
   log: StageLogger;
   discoverTools: () => Promise<ToolDefinition[]>;
+  getToolDiscoveryFailures?: () => Array<{ server: string; message: string }>;
   routeToUpstream: (request: JsonRpcRequest) => Promise<JsonRpcResponse>;
   fetchPromptIndex: () => Promise<PromptIndexEntry[]>;
   getSystemPrompt: (name: string, fallback: string) => Promise<string>;
@@ -96,6 +97,10 @@ export class PluginContextImpl implements PluginSessionContext {
     return this.deps.discoverTools();
   }
 
+  getToolDiscoveryFailures(): Array<{ server: string; message: string }> {
+    return this.deps.getToolDiscoveryFailures?.() ?? [];
+  }
+
   routeToUpstream(request: JsonRpcRequest): Promise<JsonRpcResponse> {
     return this.deps.routeToUpstream(request);
   }

src/mcplocal/src/proxymodel/plugin.ts

@@ -36,6 +36,8 @@ export interface PluginSessionContext {
 
   // Upstream access
   discoverTools(): Promise<ToolDefinition[]>;
+  /** Servers that contributed no tools on the last discoverTools run, with the error. */
+  getToolDiscoveryFailures(): Array<{ server: string; message: string }>;
   routeToUpstream(request: JsonRpcRequest): Promise<JsonRpcResponse>;
 
   // Prompt access

src/mcplocal/src/proxymodel/plugins/gate.ts

@@ -127,6 +127,7 @@ export function createGatePlugin(config: GatePluginConfig = {}): ProxyModelPlugi
             parts.push(`  ${sanitizeWireName(t.name)}`);
           }
         }
+        parts.push(...formatDiscoveryFailures(ctx.getToolDiscoveryFailures()));
       } catch {
         // Tool discovery is optional
       }
@@ -177,6 +178,22 @@ export function createGatePlugin(config: GatePluginConfig = {}): ProxyModelPlugi
   };
 }
 
+/**
+ * A partial catalog must never look like a healthy one. When attached servers
+ * contributed no tools, say so in-band — the client has no other channel to
+ * learn that six servers silently vanished from its tool list.
+ */
+function formatDiscoveryFailures(failures: Array<{ server: string; message: string }>): string[] {
+  if (failures.length === 0) return [];
+  const parts: string[] = [];
+  parts.push(`\n⚠ WARNING: ${failures.length} attached server(s) contributed NO tools to this catalog:`);
+  for (const f of failures) {
+    parts.push(`  - ${f.server}: ${f.message}`);
+  }
+  parts.push('The tool list above is INCOMPLETE. Report this to the user instead of treating a missing tool as nonexistent.');
+  return parts;
+}
+
 // ── begin_session tool definition ──
 
 function getBeginSessionTool(llmSelector: LlmPromptSelector | null): ToolDefinition {
@@ -442,6 +459,7 @@ async function handleBeginSession(
         responseParts.push(`  ${sanitizeWireName(t.name)}`);
       }
     }
+    responseParts.push(...formatDiscoveryFailures(ctx.getToolDiscoveryFailures()));
   } catch {
     // Tool discovery is optional
   }

src/mcplocal/src/router.ts

@@ -75,6 +75,8 @@ export class McpRouter {
   // `tools/list` from re-hitting slow/dead upstreams and absorbs negative results so one
   // dead server only stalls the first POST, not every subsequent one.
   private listCache = new Map<string, ListCacheEntry>();
+  /** Per-server failures from the most recent discoverTools run. */
+  private toolDiscoveryFailures: Array<{ server: string; message: string }> = [];
   private readonly LIST_CACHE_POSITIVE_TTL_MS = 30_000;
   private readonly LIST_CACHE_NEGATIVE_TTL_MS = 30_000;
 
@@ -176,6 +178,7 @@ export class McpRouter {
         error: (msg: string) => console.error(`[plugin:${sessionId.slice(0, 8)}] ${msg}`),
       },
       discoverTools: () => this.discoverTools(),
+      getToolDiscoveryFailures: () => this.getToolDiscoveryFailures(),
       routeToUpstream: (request) => this.routeNamespacedCall(request, 'name', this.toolToServer),
       fetchPromptIndex: () => this.fetchPromptIndex(),
       getSystemPrompt: (name, fallback) => this.getSystemPrompt(name, fallback),
@@ -329,7 +332,7 @@ export class McpRouter {
     const started = Date.now();
     let cachedCount = 0;
     let freshCount = 0;
-    const failed: string[] = [];
+    const failed: Array<{ server: string; message: string }> = [];
 
     // Discover tools from all servers in parallel so one slow server doesn't block the rest
     const entries = [...this.upstreams.entries()];
@@ -369,7 +372,7 @@ export class McpRouter {
         const cached = result.value.cached;
         if (cached.kind === 'err') {
           cachedCount++;
-          failed.push(serverName);
+          failed.push({ server: serverName, message: cached.message });
           continue;
         }
         response = { jsonrpc: '2.0', id: `cached-${serverName}`, result: cached.result };
@@ -381,7 +384,7 @@ export class McpRouter {
           const message = (response.error as { message?: string }).message ?? 'unknown error';
           this.setListCacheEntry(serverName, 'tools/list', { kind: 'err', message, fetchedAt: Date.now() });
           console.warn(`[discoverTools] ${serverName}: ${message}`);
-          failed.push(serverName);
+          failed.push({ server: serverName, message });
           continue;
         }
         if (response.result !== undefined) {
@@ -410,16 +413,27 @@ export class McpRouter {
       }
     }
 
+    this.toolDiscoveryFailures = failed;
+
     if (entries.length > 0) {
       const elapsed = Date.now() - started;
       const project = this.projectName ? ` project=${this.projectName}` : '';
-      const failedStr = failed.length > 0 ? ` failed=[${failed.join(',')}]` : '';
+      const failedStr = failed.length > 0 ? ` failed=[${failed.map((f) => f.server).join(',')}]` : '';
       console.info(`[discoverTools]${project} fresh=${freshCount} cached=${cachedCount}${failedStr} elapsed=${elapsed}ms`);
     }
 
     return allTools;
   }
 
+  /**
+   * Servers that contributed no tools on the most recent `discoverTools` run,
+   * with the error that silenced them. A partial catalog must never look like
+   * a healthy one: the gate reads this to warn the client in-band.
+   */
+  getToolDiscoveryFailures(): Array<{ server: string; message: string }> {
+    return this.toolDiscoveryFailures;
+  }
+
   /**
    * Discover resources from all upstreams by calling resources/list on each.
    * Shares the per-server list cache with `discoverTools`.

src/mcplocal/tests/discovery.test.ts

@@ -1,5 +1,5 @@
 import { describe, it, expect, vi } from 'vitest';
-import { refreshUpstreams } from '../src/discovery.js';
+import { refreshUpstreams, refreshProjectUpstreams } from '../src/discovery.js';
 import { McpRouter } from '../src/router.js';
 
 function mockMcpdClient(servers: Array<{ id: string; name: string; transport: string }>) {
@@ -69,3 +69,61 @@ describe('refreshUpstreams', () => {
     expect(router.getUpstreamNames()).toHaveLength(0);
   });
 });
+
+describe('refreshProjectUpstreams', () => {
+  /**
+   * Regression: a cached project router outlives the caller's bearer token.
+   * Upstreams used to be created only for NEW server names, so after a token
+   * rotation every pre-existing upstream kept posting the old token — six
+   * healthy servers 401'd on tools/list forever while newly attached ones
+   * worked. Every refresh must rebind existing upstreams to the fresh token.
+   */
+  it('rebinds existing upstreams to the current auth token on every refresh', async () => {
+    const router = new McpRouter();
+    const servers = [{ id: 'srv-1', name: 'gitea', transport: 'stdio' }];
+
+    // Base client: withToken(t) mints a child client whose posts we can count.
+    const children = new Map<string, ReturnType<typeof mockMcpdClient>>();
+    const base = mockMcpdClient(servers);
+    (base as any).forward = vi.fn(async () => ({ status: 200, body: servers }));
+    (base as any).withToken = vi.fn((t: string) => {
+      if (!children.has(t)) {
+        const child = mockMcpdClient(servers);
+        child.post = vi.fn(async () => ({ result: { tools: [{ name: 'merge_pull_request' }] } }));
+        children.set(t, child);
+      }
+      return children.get(t);
+    });
+
+    await refreshProjectUpstreams(router, base as any, 'sre', 'old-token');
+    await refreshProjectUpstreams(router, base as any, 'sre', 'new-token');
+
+    const tools = await router.discoverTools();
+    expect(tools.map((t) => t.name)).toEqual(['gitea/merge_pull_request']);
+    // The proxy call must ride the NEW token's client, not the stale one.
+    expect(children.get('new-token')!.post).toHaveBeenCalledWith('/api/v1/mcp/proxy', expect.anything());
+    expect(children.get('old-token')!.post).not.toHaveBeenCalled();
+  });
+
+  it('updates the server id when a server was recreated under the same name', async () => {
+    const router = new McpRouter();
+    const base = mockMcpdClient([]);
+    const posts: unknown[] = [];
+    const child = mockMcpdClient([]);
+    child.post = vi.fn(async (_path: string, body: unknown) => {
+      posts.push(body);
+      return { result: { tools: [] } };
+    });
+    (base as any).withToken = vi.fn(() => child);
+    (base as any).forward = vi.fn()
+      .mockResolvedValueOnce({ status: 200, body: [{ id: 'srv-old', name: 'gitea', transport: 'stdio' }] })
+      .mockResolvedValueOnce({ status: 200, body: [{ id: 'srv-new', name: 'gitea', transport: 'stdio' }] });
+
+    await refreshProjectUpstreams(router, base as any, 'sre', 't');
+    await refreshProjectUpstreams(router, base as any, 'sre', 't');
+
+    await router.discoverTools();
+    expect(posts).toHaveLength(1);
+    expect((posts[0] as { serverId: string }).serverId).toBe('srv-new');
+  });
+});