fix(mcp): fix .mcp.json, timeouts, txt outline, subprocess leaks, version pin, proxy stripping

.mcp.json

@@ -1,3 +1,9 @@
 {
-  "mcpServers": {}
+  "mcpServers": {
+    "mcp-search": {
+      "type": "stdio",
+      "command": "bun",
+      "args": ["${CLAUDE_PLUGIN_ROOT}/scripts/mcp-server.cjs"]
+    }
+  }
 }

src/servers/mcp-server.ts

@@ -104,7 +104,8 @@ const TOOL_ENDPOINT_MAP: Record<string, string> = {
  */
 async function callWorkerAPI(
   endpoint: string,
-  params: Record<string, any>
+  params: Record<string, any>,
+  timeoutMs?: number
 ): Promise<{ content: Array<{ type: 'text'; text: string }>; isError?: boolean }> {
   logger.debug('SYSTEM', '→ Worker API', undefined, { endpoint, params });
 
@@ -119,7 +120,7 @@ async function callWorkerAPI(
     }
 
     const apiPath = `${endpoint}?${searchParams}`;
-    const response = await workerHttpRequest(apiPath);
+    const response = await workerHttpRequest(apiPath, timeoutMs ? { timeoutMs } : undefined);
 
     if (!response.ok) {
       const errorText = await response.text();
@@ -149,15 +150,17 @@ async function callWorkerAPI(
  */
 async function callWorkerAPIPost(
   endpoint: string,
-  body: Record<string, any>
+  body: Record<string, any>,
+  timeoutMs?: number
 ): Promise<{ content: Array<{ type: 'text'; text: string }>; isError?: boolean }> {
   logger.debug('HTTP', 'Worker API request (POST)', undefined, { endpoint });
 
   try {
     const response = await workerHttpRequest(endpoint, {
       method: 'POST',
       headers: { 'Content-Type': 'application/json' },
-      body: JSON.stringify(body)
+      body: JSON.stringify(body),
+      ...(timeoutMs ? { timeoutMs } : {})
     });
 
     if (!response.ok) {
@@ -473,7 +476,7 @@ NEVER fetch full details without filtering first. 10x token savings.`,
       additionalProperties: true
     },
     handler: async (args: any) => {
-      return await callWorkerAPIPost('/api/corpus', args);
+      return await callWorkerAPIPost('/api/corpus', args, 120000);
     }
   },
   {
@@ -502,7 +505,7 @@ NEVER fetch full details without filtering first. 10x token savings.`,
     handler: async (args: any) => {
       const { name, ...rest } = args;
       if (typeof name !== 'string' || name.trim() === '') throw new Error('Missing required argument: name');
-      return await callWorkerAPIPost(`/api/corpus/${encodeURIComponent(name)}/prime`, rest);
+      return await callWorkerAPIPost(`/api/corpus/${encodeURIComponent(name)}/prime`, rest, 60000);
     }
   },
   {
@@ -520,7 +523,7 @@ NEVER fetch full details without filtering first. 10x token savings.`,
     handler: async (args: any) => {
       const { name, ...rest } = args;
       if (typeof name !== 'string' || name.trim() === '') throw new Error('Missing required argument: name');
-      return await callWorkerAPIPost(`/api/corpus/${encodeURIComponent(name)}/query`, rest);
+      return await callWorkerAPIPost(`/api/corpus/${encodeURIComponent(name)}/query`, rest, 60000);
     }
   },
   {
@@ -537,7 +540,7 @@ NEVER fetch full details without filtering first. 10x token savings.`,
     handler: async (args: any) => {
       const { name, ...rest } = args;
       if (typeof name !== 'string' || name.trim() === '') throw new Error('Missing required argument: name');
-      return await callWorkerAPIPost(`/api/corpus/${encodeURIComponent(name)}/rebuild`, rest);
+      return await callWorkerAPIPost(`/api/corpus/${encodeURIComponent(name)}/rebuild`, rest, 120000);
     }
   },
   {
@@ -554,7 +557,7 @@ NEVER fetch full details without filtering first. 10x token savings.`,
     handler: async (args: any) => {
       const { name, ...rest } = args;
       if (typeof name !== 'string' || name.trim() === '') throw new Error('Missing required argument: name');
-      return await callWorkerAPIPost(`/api/corpus/${encodeURIComponent(name)}/reprime`, rest);
+      return await callWorkerAPIPost(`/api/corpus/${encodeURIComponent(name)}/reprime`, rest, 60000);
     }
   }
 ];

src/services/smart-file-read/parser.ts

@@ -849,8 +849,57 @@ export function parseFile(content: string, filePath: string, projectRoot?: strin
 
   const grammarPath = resolveGrammarPathWithFallback(language, projectRoot);
   if (!grammarPath) {
+    // No tree-sitter grammar available — produce a basic fallback outline
+    // by scanning for lines that look like headers (e.g., Markdown-style #,
+    // ALL-CAPS lines, or lines ending with a colon that resemble section titles).
+    const fallbackSymbols: CodeSymbol[] = [];
+    for (let i = 0; i < lines.length; i++) {
+      const line = lines[i];
+      const trimmed = line.trim();
+      if (!trimmed) continue;
+
+      // Markdown-style headers
+      const headerMatch = trimmed.match(/^(#{1,6})\s+(.+)/);
+      if (headerMatch) {
+        fallbackSymbols.push({
+          name: headerMatch[2],
+          kind: "section",
+          signature: trimmed,
+          lineStart: i + 1,
+          lineEnd: i + 1,
+          exported: false,
+        });
+        continue;
+      }
+
+      // ALL-CAPS lines (likely section headers in plain text)
+      if (trimmed.length >= 3 && trimmed.length <= 80 && /^[A-Z][A-Z0-9 _\-]+$/.test(trimmed)) {
+        fallbackSymbols.push({
+          name: trimmed,
+          kind: "section",
+          signature: trimmed,
+          lineStart: i + 1,
+          lineEnd: i + 1,
+          exported: false,
+        });
+        continue;
+      }
+
+      // Lines ending with colon (section-title style)
+      if (trimmed.endsWith(":") && trimmed.length >= 3 && trimmed.length <= 80 && !trimmed.includes("  ")) {
+        fallbackSymbols.push({
+          name: trimmed.slice(0, -1),
+          kind: "section",
+          signature: trimmed,
+          lineStart: i + 1,
+          lineEnd: i + 1,
+          exported: false,
+        });
+      }
+    }
+
     return {
-      filePath, language, symbols: [], imports: [],
+      filePath, language, symbols: fallbackSymbols, imports: [],
       totalLines: lines.length, foldedTokenEstimate: 50,
     };
   }
@@ -907,13 +956,10 @@ export function parseFilesBatch(
   for (const [language, groupFiles] of languageGroups) {
     const grammarPath = resolveGrammarPathWithFallback(language, projectRoot);
     if (!grammarPath) {
-      // No grammar — return empty results for these files
+      // No tree-sitter grammar — use fallback parser for these files
       for (const file of groupFiles) {
-        const lines = file.content.split("\n");
-        results.set(file.relativePath, {
-          filePath: file.relativePath, language, symbols: [], imports: [],
-          totalLines: lines.length, foldedTokenEstimate: 50,
-        });
+        const fallbackResult = parseFile(file.content, file.relativePath, projectRoot);
+        results.set(file.relativePath, fallbackResult);
       }
       continue;
     }

src/services/sync/ChromaMcpManager.ts

@@ -207,7 +207,7 @@ export class ChromaMcpManager {
 
       const args = [
         '--python', pythonVersion,
-        'chroma-mcp',
+        'chroma-mcp==0.2.3',
         '--client-type', 'http',
         '--host', chromaHost,
         '--port', chromaPort
@@ -233,7 +233,7 @@ export class ChromaMcpManager {
     // Local mode: persistent client with data directory
     return [
       '--python', pythonVersion,
-      'chroma-mcp',
+      'chroma-mcp==0.2.3',
       '--client-type', 'persistent',
       '--data-dir', DEFAULT_CHROMA_DATA_DIR.replace(/\\/g, '/')
     ];
@@ -264,9 +264,14 @@ export class ChromaMcpManager {
       // Transport error: chroma-mcp subprocess likely died (e.g., killed by orphan reaper,
       // HNSW index corruption). Mark connection dead and retry once after reconnect (#1131).
       // Without this retry, callers see a one-shot error even though reconnect would succeed.
+      // IMPORTANT: Close transport BEFORE nulling to prevent subprocess leaks (#1925).
       this.connected = false;
+      const staleTransport = this.transport;
+      const staleClient = this.client;
       this.client = null;
       this.transport = null;
+      try { if (staleTransport) await staleTransport.close(); } catch { /* already dead */ }
+      try { if (staleClient) await staleClient.close(); } catch { /* already dead */ }
 
       logger.warn('CHROMA_MCP', `Transport error during "${toolName}", reconnecting and retrying once`, {
         error: transportError instanceof Error ? transportError.message : String(transportError)
@@ -354,6 +359,26 @@ export class ChromaMcpManager {
     logger.info('CHROMA_MCP', 'chroma-mcp MCP connection stopped');
   }
 
+  /**
+   * Synchronous shutdown — kills the chroma-mcp subprocess immediately.
+   * Called from process 'exit' handler where async operations are not possible.
+   * Ensures no orphaned chroma-mcp processes survive the worker.
+   */
+  shutdownSync(): void {
+    const transportRef = this.transport as unknown as { _process?: import('child_process').ChildProcess } | null;
+    const childProcess = transportRef?._process;
+    if (childProcess?.pid && !childProcess.killed) {
+      try {
+        childProcess.kill('SIGKILL');
+        logger.info('CHROMA_MCP', 'Killed chroma-mcp subprocess on shutdown', { pid: childProcess.pid });
+      } catch { /* best effort */ }
+    }
+    this.client = null;
+    this.transport = null;
+    this.connected = false;
+    this.connecting = null;
+  }
+
   /**
    * Reset the singleton instance (for testing).
    * Awaits stop() to prevent dual subprocesses.
@@ -434,15 +459,26 @@ export class ChromaMcpManager {
     }
   }
 
+  /** Proxy env var names to strip -- chroma-mcp uses local persistent storage
+   *  and doesn't need network proxies. SOCKS5 proxies in particular break the
+   *  stdio handshake by interfering with Python's HTTP client initialization. */
+  private static readonly PROXY_ENV_VARS_TO_STRIP = new Set([
+    'ALL_PROXY', 'all_proxy',
+    'HTTP_PROXY', 'http_proxy',
+    'HTTPS_PROXY', 'https_proxy',
+    'NO_PROXY', 'no_proxy',
+  ]);
+
   /**
    * Build subprocess environment with SSL certificate overrides for enterprise proxy compatibility.
+   * Strips proxy env vars that break chroma-mcp's stdio handshake (#1927).
    * If a combined cert bundle exists (Zscaler), injects SSL_CERT_FILE, REQUESTS_CA_BUNDLE, etc.
    * Otherwise returns a plain string-keyed copy of process.env.
    */
   private getSpawnEnv(): Record<string, string> {
     const baseEnv: Record<string, string> = {};
     for (const [key, value] of Object.entries(sanitizeEnv(process.env))) {
-      if (value !== undefined) {
+      if (value !== undefined && !ChromaMcpManager.PROXY_ENV_VARS_TO_STRIP.has(key)) {
         baseEnv[key] = value;
       }
     }
@@ -482,3 +518,12 @@ export class ChromaMcpManager {
     });
   }
 }
+
+// Safety net: kill chroma-mcp subprocess on process exit to prevent orphans.
+// The 'exit' event is the last chance to clean up — only synchronous code runs here.
+process.on('exit', () => {
+  const instance = ChromaMcpManager['instance'];
+  if (instance) {
+    instance.shutdownSync();
+  }
+});