@colbymchenry/codegraph-darwin-x64 0.9.3 → 0.9.5

package/lib/dist/mcp/index.js.map

@@ -1 +1 @@
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package/lib/dist/mcp/proxy.d.ts

@@ -0,0 +1,46 @@
+/**
+ * MCP proxy mode — issue #411.
+ *
+ * The proxy is a near-transparent stdio↔socket pipe. Once it has verified
+ * the daemon's hello line (same major.minor.patch as ours), it does no
+ * protocol parsing of its own: every byte the MCP host writes to the proxy's
+ * stdin goes straight to the daemon socket, and every byte the daemon emits
+ * goes straight to the host's stdout. Server-initiated JSON-RPC requests
+ * (e.g. `roots/list`) flow through the same pipe transparently.
+ *
+ * Lifecycle expectations:
+ *   - The proxy exits when *either* stream closes (host stdin closed →
+ *     daemon socket end, or daemon-side socket close → host stdout end).
+ *   - Closing the socket on the proxy side is what tells the daemon to
+ *     decrement its connected-clients refcount.
+ *   - On a parent-process death we can't detect via stdin close (e.g. SIGKILL
+ *     of the MCP host), the proxy's PPID watchdog catches it — same logic
+ *     the direct-mode server uses; see issue #277.
+ */
+export interface ProxyResult {
+    /**
+     * `proxied` — successfully attached to a same-version daemon and piped
+     * stdio. The proxy stays alive until either end closes.
+     * `fallback-needed` — the daemon rejected us (version mismatch / unreachable
+     * socket) and the caller should run the server in direct mode.
+     */
+    outcome: 'proxied' | 'fallback-needed';
+    reason?: string;
+}
+/**
+ * Attempt to connect to the daemon at `socketPath` and pipe stdio through it.
+ *
+ * Returns a promise that resolves when either:
+ *   - the connection succeeded and one of stdin/socket has now closed
+ *     (after which the process should exit), or
+ *   - the connection failed early enough that the caller can still fall
+ *     back to direct mode.
+ *
+ * The `expectedVersion` param defaults to the package's own version — daemon
+ * and proxy MUST match exactly. Mismatch resolves with
+ * `outcome: 'fallback-needed'` so the caller can transparently start its own
+ * server. (We accept the cost of two concurrent servers in this case as the
+ * price of never silently running a stale daemon against newer client code.)
+ */
+export declare function runProxy(socketPath: string, expectedVersion?: string): Promise<ProxyResult>;
+//# sourceMappingURL=proxy.d.ts.map

package/lib/dist/mcp/proxy.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"proxy.d.ts","sourceRoot":"","sources":["../../src/mcp/proxy.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAWH,MAAM,WAAW,WAAW;IAC1B;;;;;OAKG;IACH,OAAO,EAAE,SAAS,GAAG,iBAAiB,CAAC;IACvC,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED;;;;;;;;;;;;;;GAcG;AACH,wBAAsB,QAAQ,CAC5B,UAAU,EAAE,MAAM,EAClB,eAAe,GAAE,MAAgC,GAChD,OAAO,CAAC,WAAW,CAAC,CAsCtB"}

package/lib/dist/mcp/proxy.js

@@ -0,0 +1,276 @@
+"use strict";
+/**
+ * MCP proxy mode — issue #411.
+ *
+ * The proxy is a near-transparent stdio↔socket pipe. Once it has verified
+ * the daemon's hello line (same major.minor.patch as ours), it does no
+ * protocol parsing of its own: every byte the MCP host writes to the proxy's
+ * stdin goes straight to the daemon socket, and every byte the daemon emits
+ * goes straight to the host's stdout. Server-initiated JSON-RPC requests
+ * (e.g. `roots/list`) flow through the same pipe transparently.
+ *
+ * Lifecycle expectations:
+ *   - The proxy exits when *either* stream closes (host stdin closed →
+ *     daemon socket end, or daemon-side socket close → host stdout end).
+ *   - Closing the socket on the proxy side is what tells the daemon to
+ *     decrement its connected-clients refcount.
+ *   - On a parent-process death we can't detect via stdin close (e.g. SIGKILL
+ *     of the MCP host), the proxy's PPID watchdog catches it — same logic
+ *     the direct-mode server uses; see issue #277.
+ */
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.runProxy = runProxy;
+const fs = __importStar(require("fs"));
+const net = __importStar(require("net"));
+const wasm_runtime_flags_1 = require("../extraction/wasm-runtime-flags");
+const daemon_1 = require("./daemon");
+const version_1 = require("./version");
+/** Default poll cadence for the PPID watchdog (same as the direct server). */
+const DEFAULT_PPID_POLL_MS = 5000;
+/**
+ * Attempt to connect to the daemon at `socketPath` and pipe stdio through it.
+ *
+ * Returns a promise that resolves when either:
+ *   - the connection succeeded and one of stdin/socket has now closed
+ *     (after which the process should exit), or
+ *   - the connection failed early enough that the caller can still fall
+ *     back to direct mode.
+ *
+ * The `expectedVersion` param defaults to the package's own version — daemon
+ * and proxy MUST match exactly. Mismatch resolves with
+ * `outcome: 'fallback-needed'` so the caller can transparently start its own
+ * server. (We accept the cost of two concurrent servers in this case as the
+ * price of never silently running a stale daemon against newer client code.)
+ */
+async function runProxy(socketPath, expectedVersion = version_1.CodeGraphPackageVersion) {
+    // POSIX: refuse to connect to a stale socket file that points at no
+    // listening process. `fs.existsSync` is a cheap pre-check; a real
+    // ECONNREFUSED below catches the rare "exists but unbound" race.
+    if (process.platform !== 'win32' && !fs.existsSync(socketPath)) {
+        return { outcome: 'fallback-needed', reason: 'socket file missing' };
+    }
+    const socket = net.createConnection(socketPath);
+    socket.setEncoding('utf8');
+    const hello = await readHelloLine(socket).catch((err) => {
+        socket.destroy();
+        return new Error(String(err));
+    });
+    if (hello instanceof Error) {
+        return { outcome: 'fallback-needed', reason: hello.message };
+    }
+    if (hello.codegraph !== expectedVersion) {
+        process.stderr.write(`[CodeGraph MCP] Found a daemon on ${socketPath} but version (${hello.codegraph}) ` +
+            `differs from ours (${expectedVersion}); falling back to direct mode.\n`);
+        socket.destroy();
+        return { outcome: 'fallback-needed', reason: 'version mismatch' };
+    }
+    process.stderr.write(`[CodeGraph MCP] Attached to shared daemon on ${socketPath} (pid ${hello.pid}, v${hello.codegraph}).\n`);
+    startPpidWatchdog(socket);
+    await pipeUntilClose(socket);
+    // Host disconnected (or the daemon went away). The proxy's only job is the
+    // pipe; exit now so we don't linger — process.stdin's 'data' listener would
+    // otherwise keep the event loop alive and leave a zombie launcher behind.
+    process.exit(0);
+}
+/**
+ * Read one CRLF/LF-terminated JSON line from the socket, parse it as the
+ * daemon hello, and return it. Bounded to {@link MAX_HELLO_LINE_BYTES} so a
+ * malicious or broken peer can't OOM us. Times out at 3s — a healthy daemon
+ * sends hello immediately on accept.
+ */
+function readHelloLine(socket) {
+    return new Promise((resolve, reject) => {
+        let buffer = '';
+        const cleanup = () => {
+            socket.removeListener('data', onData);
+            socket.removeListener('error', onError);
+            socket.removeListener('close', onClose);
+            clearTimeout(timer);
+        };
+        const onData = (chunk) => {
+            buffer += typeof chunk === 'string' ? chunk : chunk.toString('utf8');
+            const idx = buffer.indexOf('\n');
+            if (idx === -1) {
+                if (buffer.length > daemon_1.MAX_HELLO_LINE_BYTES) {
+                    cleanup();
+                    reject(new Error('daemon hello line exceeded size limit'));
+                }
+                return;
+            }
+            const line = buffer.slice(0, idx);
+            // Re-emit anything past the newline so the pipe-stage sees it.
+            const tail = buffer.slice(idx + 1);
+            cleanup();
+            if (tail.length > 0) {
+                // Push back via unshift — Node's net.Socket supports it on readable streams.
+                socket.unshift(tail);
+            }
+            try {
+                const parsed = JSON.parse(line);
+                if (typeof parsed.codegraph !== 'string' || typeof parsed.pid !== 'number') {
+                    reject(new Error('daemon hello missing required fields'));
+                    return;
+                }
+                resolve(parsed);
+            }
+            catch (err) {
+                reject(new Error(`daemon hello not JSON: ${err instanceof Error ? err.message : String(err)}`));
+            }
+        };
+        const onError = (err) => { cleanup(); reject(err); };
+        const onClose = () => { cleanup(); reject(new Error('daemon closed connection before hello')); };
+        const timer = setTimeout(() => {
+            cleanup();
+            reject(new Error('timed out waiting for daemon hello'));
+        }, 3000);
+        timer.unref?.();
+        socket.on('data', onData);
+        socket.on('error', onError);
+        socket.on('close', onClose);
+    });
+}
+/**
+ * Pipe stdin → socket and socket → stdout. Resolves once either end closes
+ * so the process can exit. Note: we deliberately do NOT use
+ * `process.stdin.pipe(socket)` because pipe propagates 'end' onto the
+ * downstream, which would close the socket prematurely if stdin happens to
+ * end early — the MCP spec allows it to stay open across reconnects.
+ */
+function pipeUntilClose(socket) {
+    return new Promise((resolve) => {
+        let resolved = false;
+        const done = () => { if (!resolved) {
+            resolved = true;
+            resolve();
+        } };
+        process.stdin.on('data', (chunk) => {
+            try {
+                socket.write(chunk);
+            }
+            catch { /* socket may have errored — close path catches it */ }
+        });
+        process.stdin.on('end', () => {
+            try {
+                socket.end();
+            }
+            catch { /* ignore */ }
+            done();
+        });
+        process.stdin.on('close', () => {
+            try {
+                socket.destroy();
+            }
+            catch { /* ignore */ }
+            done();
+        });
+        socket.on('data', (chunk) => {
+            try {
+                process.stdout.write(chunk);
+            }
+            catch { /* ignore */ }
+        });
+        socket.on('end', () => done());
+        socket.on('close', () => done());
+        socket.on('error', (err) => {
+            process.stderr.write(`[CodeGraph MCP] daemon socket error: ${err.message}\n`);
+            done();
+        });
+    });
+}
+/**
+ * PPID watchdog mirroring the one in `MCPServer.start` — kills the proxy if
+ * the MCP host (or its proxy of a host, see HOST_PPID_ENV) goes away without
+ * closing stdin. Issue #277 documents why we can't rely on stdin EOF on
+ * Linux: the parent may be SIGKILL'd and reparenting doesn't close pipes.
+ *
+ * The proxy's "kill" is just a socket close + process.exit — no SQLite or
+ * watchers to clean up, so this is cheap.
+ */
+function startPpidWatchdog(socket) {
+    const pollMs = parsePollMs(process.env.CODEGRAPH_PPID_POLL_MS);
+    if (pollMs <= 0)
+        return;
+    const originalPpid = process.ppid;
+    const hostPpid = parseHostPpid(process.env[wasm_runtime_flags_1.HOST_PPID_ENV]);
+    const timer = setInterval(() => {
+        const current = process.ppid;
+        const ppidChanged = current !== originalPpid;
+        const hostGone = hostPpid !== null && !isProcessAliveLocal(hostPpid);
+        if (ppidChanged || hostGone) {
+            const reason = ppidChanged
+                ? `ppid ${originalPpid} -> ${current}`
+                : `host pid ${hostPpid} exited`;
+            process.stderr.write(`[CodeGraph MCP] Parent process exited (${reason}); shutting down.\n`);
+            try {
+                socket.destroy();
+            }
+            catch { /* ignore */ }
+            process.exit(0);
+        }
+    }, pollMs);
+    timer.unref?.();
+}
+function parsePollMs(raw) {
+    if (raw === undefined || raw === '')
+        return DEFAULT_PPID_POLL_MS;
+    const parsed = Number(raw);
+    if (!Number.isFinite(parsed))
+        return DEFAULT_PPID_POLL_MS;
+    if (parsed < 0)
+        return DEFAULT_PPID_POLL_MS;
+    return Math.floor(parsed);
+}
+function parseHostPpid(raw) {
+    if (raw === undefined || raw === '')
+        return null;
+    const parsed = Number(raw);
+    if (!Number.isInteger(parsed) || parsed <= 1)
+        return null;
+    return parsed;
+}
+function isProcessAliveLocal(pid) {
+    try {
+        process.kill(pid, 0);
+        return true;
+    }
+    catch (err) {
+        const e = err;
+        if (e.code === 'EPERM')
+            return true;
+        return false;
+    }
+}
+//# sourceMappingURL=proxy.js.map

package/lib/dist/mcp/proxy.js.map

@@ -0,0 +1 @@
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package/lib/dist/mcp/server-instructions.d.ts

@@ -15,5 +15,5 @@
  * burn tokens. Reference only tools that exist on `main`; gate any
  * conditional tools behind feature checks if/when they ship.
  */
-export declare const SERVER_INSTRUCTIONS = "# Codegraph \u2014 code intelligence over an indexed knowledge graph\n\nCodegraph is a SQLite knowledge graph of every symbol, edge, and file\nin the workspace. Reads are sub-millisecond; the index lags writes by\nabout a second through the file watcher. Consult it BEFORE writing or\nediting code, not during.\n\n## Answer directly \u2014 don't delegate exploration\n\nFor \"how does X work\", architecture, trace, or where-is-X questions,\nanswer DIRECTLY using 2-3 codegraph calls: `codegraph_context` first,\nthen ONE `codegraph_explore` for the source of the symbols it surfaces.\nCodegraph IS the pre-built search index \u2014 so delegating the lookup to a\nseparate file-reading sub-task/agent, or running your own grep + read\nloop, repeats work codegraph already did and costs more for the same\nanswer. Reach for raw Read/Grep only to confirm a specific detail\ncodegraph didn't cover. A direct codegraph answer is typically a handful\nof calls; a grep/read exploration is dozens.\n\n## Tool selection by intent\n\n- **\"What is the symbol named X?\"** \u2192 `codegraph_search`\n- **\"What's the deal with this task / feature / area?\"** \u2192 `codegraph_context` (PRIMARY \u2014 composes search + node + callers + callees in one call)\n- **\"What calls this?\"** \u2192 `codegraph_callers`\n- **\"What does this call?\"** \u2192 `codegraph_callees`\n- **\"What would changing this break?\"** \u2192 `codegraph_impact`\n- **\"Show me this symbol's source / signature / docstring.\"** \u2192 `codegraph_node`\n- **\"Show me several related symbols' source / survey an area.\"** \u2192 `codegraph_explore` (ONE capped call; prefer over many codegraph_node/Read)\n- **\"What's in directory X?\"** \u2192 `codegraph_files`\n- **\"Is the index ready / what's its size?\"** \u2192 `codegraph_status`\n\n## Common chains\n\n- **Onboarding**: `codegraph_context` first. If still unclear, `codegraph_explore` for breadth, then `codegraph_node` on specific symbols.\n- **Refactor planning**: `codegraph_search` \u2192 `codegraph_callers` \u2192 `codegraph_impact`. The blast-radius answer comes from impact, not from walking callers manually.\n- **Debugging a regression**: `codegraph_callers` of the suspected symbol; widen with `codegraph_impact` if an unexpected call appears.\n\n## Anti-patterns\n\n- **Don't grep first** when looking up a symbol by name \u2014 `codegraph_search` is faster and returns kind + location + signature.\n- **Don't chain `codegraph_search` + `codegraph_node`** when you just want context \u2014 `codegraph_context` is one round-trip.\n- **Don't loop `codegraph_node` over many symbols** \u2014 one `codegraph_explore` call returns them all grouped by file, while each separate call re-reads the whole context and costs far more. Use `codegraph_node` for a single symbol.\n- **Don't query the index immediately after editing a file** \u2014 the watcher needs ~500ms to debounce + sync. Wait for the next turn.\n\n## Limitations\n\n- Index lags file writes by ~1 second.\n- Cross-file resolution is best-effort name matching; ambiguous calls may return multiple candidates.\n- No live correctness validation \u2014 that's still the TypeScript compiler / test suite / linter's job. Codegraph supplements those with structural context they don't have.\n";
+export declare const SERVER_INSTRUCTIONS = "# Codegraph \u2014 code intelligence over an indexed knowledge graph\n\nCodegraph is a SQLite knowledge graph of every symbol, edge, and file\nin the workspace. Reads are sub-millisecond; the index lags writes by\nabout a second through the file watcher. Consult it BEFORE writing or\nediting code, not during.\n\n## Answer directly \u2014 don't delegate exploration\n\nFor \"how does X work\", architecture, trace, or where-is-X questions,\nanswer DIRECTLY using 2-3 codegraph calls: `codegraph_context` first,\nthen ONE `codegraph_explore` for the source of the symbols it surfaces.\nCodegraph IS the pre-built search index \u2014 so delegating the lookup to a\nseparate file-reading sub-task/agent, or running your own grep + read\nloop, repeats work codegraph already did and costs more for the same\nanswer. Reach for raw Read/Grep only to confirm a specific detail\ncodegraph didn't cover. A direct codegraph answer is typically a handful\nof calls; a grep/read exploration is dozens.\n\n## Tool selection by intent\n\n- **\"What is the symbol named X?\"** \u2192 `codegraph_search`\n- **\"What's the deal with this task / feature / area?\"** \u2192 `codegraph_context` (PRIMARY \u2014 composes search + node + callers + callees in one call)\n- **\"How does X reach/become Y? / trace the flow / the path from X to Y\"** \u2192 `codegraph_trace` (ONE call returns the whole call path, including dynamic-dispatch hops \u2014 callbacks, React re-render, JSX children \u2014 that grep can't follow)\n- **\"What calls this?\"** \u2192 `codegraph_callers`\n- **\"What does this call?\"** \u2192 `codegraph_callees`\n- **\"What would changing this break?\"** \u2192 `codegraph_impact`\n- **\"Show me this symbol's source / signature / docstring.\"** \u2192 `codegraph_node`\n- **\"Show me several related symbols' source / survey an area.\"** \u2192 `codegraph_explore` (ONE capped call; prefer over many codegraph_node/Read)\n- **\"What's in directory X?\"** \u2192 `codegraph_files`\n- **\"Is the index ready / what's its size?\"** \u2192 `codegraph_status`\n\n## Common chains\n\n- **Flow / \"how does X reach Y\"**: `codegraph_trace` from\u2192to FIRST \u2014 one call returns the entire path with dynamic-dispatch hops bridged. Then ONE `codegraph_explore` for the hop bodies if you need them. Do NOT reconstruct the path with `codegraph_search` + `codegraph_callers` \u2014 that's exactly what trace does in a single call.\n- **Onboarding**: `codegraph_context` first. If still unclear, `codegraph_explore` for breadth, then `codegraph_node` on specific symbols.\n- **Refactor planning**: `codegraph_search` \u2192 `codegraph_callers` \u2192 `codegraph_impact`. The blast-radius answer comes from impact, not from walking callers manually.\n- **Debugging a regression**: `codegraph_callers` of the suspected symbol; widen with `codegraph_impact` if an unexpected call appears.\n\n## Anti-patterns\n\n- **Don't grep first** when looking up a symbol by name \u2014 `codegraph_search` is faster and returns kind + location + signature.\n- **Don't chain `codegraph_search` + `codegraph_node`** when you just want context \u2014 `codegraph_context` is one round-trip.\n- **Don't loop `codegraph_node` over many symbols** \u2014 one `codegraph_explore` call returns them all grouped by file, while each separate call re-reads the whole context and costs far more. Use `codegraph_node` for a single symbol.\n- **After editing, check the staleness banner.** When a tool response starts with \"\u26A0\uFE0F Some files referenced below were edited since the last index sync\u2026\", the listed files are pending re-index \u2014 Read those specific files for accurate content. Every file NOT in that banner is fresh, so still trust codegraph. `codegraph_status` also lists pending files under \"Pending sync\".\n\n## Limitations\n\n- Index lags file writes by ~1 second.\n- Cross-file resolution is best-effort name matching; ambiguous calls may return multiple candidates.\n- No live correctness validation \u2014 that's still the TypeScript compiler / test suite / linter's job. Codegraph supplements those with structural context they don't have.\n";
 //# sourceMappingURL=server-instructions.d.ts.map

package/lib/dist/mcp/server-instructions.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"server-instructions.d.ts","sourceRoot":"","sources":["../../src/mcp/server-instructions.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AACH,eAAO,MAAM,mBAAmB,wtGAiD/B,CAAC"}
+{"version":3,"file":"server-instructions.d.ts","sourceRoot":"","sources":["../../src/mcp/server-instructions.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AACH,eAAO,MAAM,mBAAmB,sjIAmD/B,CAAC"}

package/lib/dist/mcp/server-instructions.js

@@ -41,6 +41,7 @@ of calls; a grep/read exploration is dozens.
 
 - **"What is the symbol named X?"** → \`codegraph_search\`
 - **"What's the deal with this task / feature / area?"** → \`codegraph_context\` (PRIMARY — composes search + node + callers + callees in one call)
+- **"How does X reach/become Y? / trace the flow / the path from X to Y"** → \`codegraph_trace\` (ONE call returns the whole call path, including dynamic-dispatch hops — callbacks, React re-render, JSX children — that grep can't follow)
 - **"What calls this?"** → \`codegraph_callers\`
 - **"What does this call?"** → \`codegraph_callees\`
 - **"What would changing this break?"** → \`codegraph_impact\`
@@ -51,6 +52,7 @@ of calls; a grep/read exploration is dozens.
 
 ## Common chains
 
+- **Flow / "how does X reach Y"**: \`codegraph_trace\` from→to FIRST — one call returns the entire path with dynamic-dispatch hops bridged. Then ONE \`codegraph_explore\` for the hop bodies if you need them. Do NOT reconstruct the path with \`codegraph_search\` + \`codegraph_callers\` — that's exactly what trace does in a single call.
 - **Onboarding**: \`codegraph_context\` first. If still unclear, \`codegraph_explore\` for breadth, then \`codegraph_node\` on specific symbols.
 - **Refactor planning**: \`codegraph_search\` → \`codegraph_callers\` → \`codegraph_impact\`. The blast-radius answer comes from impact, not from walking callers manually.
 - **Debugging a regression**: \`codegraph_callers\` of the suspected symbol; widen with \`codegraph_impact\` if an unexpected call appears.
@@ -60,7 +62,7 @@ of calls; a grep/read exploration is dozens.
 - **Don't grep first** when looking up a symbol by name — \`codegraph_search\` is faster and returns kind + location + signature.
 - **Don't chain \`codegraph_search\` + \`codegraph_node\`** when you just want context — \`codegraph_context\` is one round-trip.
 - **Don't loop \`codegraph_node\` over many symbols** — one \`codegraph_explore\` call returns them all grouped by file, while each separate call re-reads the whole context and costs far more. Use \`codegraph_node\` for a single symbol.
-- **Don't query the index immediately after editing a file** — the watcher needs ~500ms to debounce + sync. Wait for the next turn.
+- **After editing, check the staleness banner.** When a tool response starts with "⚠️ Some files referenced below were edited since the last index sync…", the listed files are pending re-index — Read those specific files for accurate content. Every file NOT in that banner is fresh, so still trust codegraph. \`codegraph_status\` also lists pending files under "Pending sync".
 
 ## Limitations
 

package/lib/dist/mcp/server-instructions.js.map

@@ -1 +1 @@
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+{"version":3,"file":"server-instructions.js","sourceRoot":"","sources":["../../src/mcp/server-instructions.ts"],"names":[],"mappings":";;;AAAA;;;;;;;;;;;;;;;;GAgBG;AACU,QAAA,mBAAmB,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAmDlC,CAAC"}

package/lib/dist/mcp/session.d.ts

@@ -0,0 +1,67 @@
+/**
+ * MCP per-connection session — speaks the JSON-RPC protocol (initialize,
+ * tools/list, tools/call) over a single {@link JsonRpcTransport}. It owns
+ * per-client state only (which protocol version the client asked for, whether
+ * it advertised `roots`, the one-shot roots/list latch); the heavyweight
+ * resources (CodeGraph, watcher, ToolHandler) live in the shared
+ * {@link MCPEngine} so daemon mode can collapse N inotify sets / DB handles
+ * to one.
+ *
+ * The state-machine itself mirrors what `MCPServer` used to do inline before
+ * issue #411 split it out — the same regression tests in
+ * `__tests__/mcp-initialize.test.ts` still drive this code path.
+ */
+import { JsonRpcTransport } from './transport';
+import { MCPEngine } from './engine';
+export interface MCPSessionOptions {
+    /**
+     * Explicit project path from the `--path` CLI flag. When set, the session
+     * will not bother asking the client for `roots/list` — we already know
+     * where the project lives.
+     */
+    explicitProjectPath?: string | null;
+}
+/**
+ * One MCP client's view of the server. Created fresh per stdio launch
+ * (direct mode) or per socket connection (daemon mode).
+ */
+export declare class MCPSession {
+    private transport;
+    private engine;
+    private clientSupportsRoots;
+    private rootsAttempted;
+    private resolvePromise;
+    private explicitProjectPath;
+    constructor(transport: JsonRpcTransport, engine: MCPEngine, opts?: MCPSessionOptions);
+    /**
+     * Start handling messages from the transport. Returns immediately — the
+     * session lives for as long as the transport is open.
+     */
+    start(): void;
+    /**
+     * Tear down the session. Does NOT touch the engine (the engine may serve
+     * other sessions) or call `process.exit` (the daemon decides when to exit).
+     */
+    stop(): void;
+    /** Underlying transport — exposed for daemon-side close hooks. */
+    getTransport(): JsonRpcTransport;
+    private handleMessage;
+    private handleInitialize;
+    private handleToolsList;
+    private handleToolsCall;
+    /**
+     * Lazy default-project resolution. Three layers:
+     *   1. await the in-flight init kicked off from `handleInitialize` (if any);
+     *   2. if still uninitialized and we never asked the client for its roots,
+     *      do so now (one-shot); fall back to cwd if the client lacks roots;
+     *   3. last-resort: re-walk from the best candidate — picks up projects
+     *      that were `codegraph init`'d *after* the server started.
+     */
+    private retryInitIfNeeded;
+    /**
+     * Ask the client for its workspace root via `roots/list` and open the
+     * first one. Falls back to `process.cwd()` on timeout or empty answer.
+     */
+    private initFromRoots;
+}
+//# sourceMappingURL=session.d.ts.map

package/lib/dist/mcp/session.d.ts.map

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