@colbymchenry/codegraph-darwin-x64 0.9.3 → 0.9.4

package/lib/dist/mcp/index.js

@@ -56,6 +56,7 @@ const sync_1 = require("../sync");
 const transport_1 = require("./transport");
 const tools_1 = require("./tools");
 const server_instructions_1 = require("./server-instructions");
+const wasm_runtime_flags_1 = require("../extraction/wasm-runtime-flags");
 /**
  * Convert a file:// URI to a filesystem path.
  * Handles URL encoding and Windows drive letter paths.
@@ -91,6 +92,53 @@ const PROTOCOL_VERSION = '2024-11-05';
  * and falling back to the process cwd.
  */
 const ROOTS_LIST_TIMEOUT_MS = 5000;
+/**
+ * How often to poll `process.ppid` to detect parent process death (see #277).
+ * 5s is a deliberate trade-off: the failure mode being guarded against is rare
+ * (parent SIGKILL'd), and longer poll = less wakeup overhead while idle.
+ */
+const DEFAULT_PPID_POLL_MS = 5000;
+/**
+ * Resolve the PPID watchdog poll interval from an env override. A value of
+ * `0` disables the watchdog entirely (escape hatch for embedded scenarios
+ * where the parent legitimately re-parents the server on purpose). Anything
+ * non-numeric or negative falls back to the default.
+ */
+function parsePpidPollMs(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);
+}
+/**
+ * Parse the host PID propagated across the `--liftoff-only` re-exec
+ * ({@link HOST_PPID_ENV}). Returns a positive integer PID, or null when
+ * unset/invalid — the direct-launch path, where the watchdog falls back to
+ * `process.ppid` divergence. PIDs of 0/1 are rejected (0 = unknown, 1 = init,
+ * i.e. already orphaned), so the watchdog doesn't latch onto init.
+ */
+function parseHostPpid(raw) {
+    if (raw === undefined || raw === '')
+        return null;
+    const parsed = Number(raw);
+    if (!Number.isInteger(parsed) || parsed <= 1)
+        return null;
+    return parsed;
+}
+/** True if a process with `pid` currently exists (signal-0 probe). */
+function isProcessAlive(pid) {
+    try {
+        process.kill(pid, 0);
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
 /**
  * Extract the first usable filesystem path from a `roots/list` result.
  * Shape per MCP spec: `{ roots: [{ uri: "file:///path", name?: string }] }`.
@@ -128,6 +176,19 @@ class MCPServer {
     // Guards the one-shot deferred resolution (roots/list or cwd) so we don't
     // re-issue roots/list on every tool call.
     rootsAttempted = false;
+    // PPID watchdog — see start(). Captured at construction so we always have a
+    // baseline, even if start() runs after a fork-style reparent.
+    originalPpid = process.ppid;
+    // The MCP host's PID, propagated across the `--liftoff-only` re-exec (see
+    // HOST_PPID_ENV). When set, the watchdog polls it directly: the re-exec
+    // inserts an intermediate process whose *death* — not just our reparenting —
+    // is what we'd otherwise miss. null on the direct (bundled) launch path.
+    hostPpid = parseHostPpid(process.env[wasm_runtime_flags_1.HOST_PPID_ENV]);
+    ppidWatchdog = null;
+    // Idempotency guard for stop(). Without it, the watchdog can race with the
+    // stdin `end`/`close` handlers (or SIGTERM/SIGINT) and double-close cg and
+    // the transport before process.exit() lands.
+    stopped = false;
     constructor(projectPath) {
         this.projectPath = projectPath || null;
         this.transport = new transport_1.StdioTransport();
@@ -151,6 +212,35 @@ class MCPServer {
         // Detect this and shut down gracefully to prevent orphaned processes.
         process.stdin.on('end', () => this.stop());
         process.stdin.on('close', () => this.stop());
+        // PPID watchdog (#277). Linux doesn't propagate parent death to children,
+        // so when the MCP host (Claude Code, opencode, …) is SIGKILL'd by the OOM
+        // killer / a force-quit / a container teardown, the child is reparented to
+        // init/systemd and the stdin `end`/`close` events don't always fire. The
+        // server would then linger indefinitely, holding inotify watches, file
+        // descriptors, and the SQLite WAL. Poll `process.ppid` and shut down the
+        // moment it changes from what we observed at startup. Cross-platform:
+        // reparenting changes ppid on Linux *and* macOS; on Windows the value can
+        // also drop to 0 once the parent is gone. When the CLI re-execs itself for
+        // `--liftoff-only`, an intermediate process sits between us and the host and
+        // outlives it, so our own ppid wouldn't change — in that case we poll the
+        // host PID (propagated via HOST_PPID_ENV) for liveness instead. The watchdog
+        // is `.unref()`'d so it never holds the event loop open on its own.
+        const pollMs = parsePpidPollMs(process.env.CODEGRAPH_PPID_POLL_MS);
+        if (pollMs > 0) {
+            this.ppidWatchdog = setInterval(() => {
+                const current = process.ppid;
+                const ppidChanged = current !== this.originalPpid;
+                const hostGone = this.hostPpid !== null && !isProcessAlive(this.hostPpid);
+                if (ppidChanged || hostGone) {
+                    const reason = ppidChanged
+                        ? `ppid ${this.originalPpid} -> ${current}`
+                        : `host pid ${this.hostPpid} exited`;
+                    process.stderr.write(`[CodeGraph MCP] Parent process exited (${reason}); shutting down.\n`);
+                    this.stop();
+                }
+            }, pollMs);
+            this.ppidWatchdog.unref();
+        }
     }
     /**
      * Try to initialize CodeGraph for the default project.
@@ -306,6 +396,13 @@ class MCPServer {
      * Stop the server
      */
     stop() {
+        if (this.stopped)
+            return;
+        this.stopped = true;
+        if (this.ppidWatchdog) {
+            clearInterval(this.ppidWatchdog);
+            this.ppidWatchdog = null;
+        }
         // Close all cached cross-project connections first
         this.toolHandler.closeAll();
         // Close the main CodeGraph instance

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

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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- **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";
 //# 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,gzHAmD/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.

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

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

@@ -112,10 +112,22 @@ export declare class ToolHandler {
      * Whether a default CodeGraph instance is available
      */
     hasDefaultCodeGraph(): boolean;
+    /**
+     * Optional allowlist of exposed tools, parsed from the CODEGRAPH_MCP_TOOLS
+     * env var (comma-separated short names, e.g. "trace,search,node,context").
+     * Unset/empty → every tool is exposed. Lets an operator (or an A/B harness)
+     * trim the tool surface without rebuilding the client config; the ablated
+     * tool is then truly absent from ListTools rather than merely denied on call.
+     * Matching is on the short form, so "trace" and "codegraph_trace" both work.
+     */
+    private toolAllowlist;
+    /** Whether a tool name passes the CODEGRAPH_MCP_TOOLS allowlist (if any). */
+    private isToolAllowed;
     /**
      * Get tool definitions with dynamic descriptions based on project size.
      * The codegraph_explore tool description includes a budget recommendation
-     * scaled to the number of indexed files.
+     * scaled to the number of indexed files. Honors the CODEGRAPH_MCP_TOOLS
+     * allowlist so a trimmed surface is reflected in ListTools.
      */
     getTools(): ToolDefinition[];
     /**
@@ -133,9 +145,19 @@ export declare class ToolHandler {
      */
     closeAll(): void;
     /**
-     * Validate that a value is a non-empty string
+     * Validate that a value is a non-empty string within length bounds.
+     *
+     * The `maxLength` cap protects against MCP clients that ship huge
+     * payloads (10MB+ query strings either by accident or maliciously).
+     * Without this, a single oversized input can pin the FTS5 index or
+     * exhaust memory before any real work runs.
      */
     private validateString;
+    /**
+     * Validate an optional path-like string input. Returns the value if
+     * valid (or undefined), or a ToolResult with the error.
+     */
+    private validateOptionalPath;
     /**
      * Execute a tool by name
      */
@@ -164,6 +186,53 @@ export declare class ToolHandler {
      * Handle codegraph_impact
      */
     private handleImpact;
+    /**
+     * Handle codegraph_trace — shortest CALL PATH between two symbols.
+     *
+     * Exposes GraphTraverser.findPath: the chain of functions from `from` to `to`,
+     * each hop annotated with file:line and the call-site line. This is the
+     * capability grep/Read structurally cannot provide. When no static path
+     * exists, the chain has almost certainly broken at dynamic dispatch
+     * (callbacks, descriptors, metaclasses) — we say so and surface the start
+     * symbol's outgoing calls so the agent bridges the one missing hop with
+     * codegraph_node rather than blindly reading.
+     */
+    private handleTrace;
+    /**
+     * Describe a synthesized (dynamic-dispatch) edge for human output: how the
+     * callback was wired up — the bridge static parsing can't see. Returns null
+     * for ordinary static edges. Used by trace + the node trail so a synthesized
+     * hop reads as "registered via onUpdate at App.tsx:3148", not a bare arrow.
+     */
+    private synthEdgeNote;
+    /**
+     * Read one trimmed source line at "relpath:line" (relative to the project
+     * root). `cache` holds split file contents so a multi-hop trace reads each
+     * file at most once. Returns null if the file/line can't be resolved.
+     */
+    private sourceLineAt;
+    /**
+     * Read a hop's body — filePath lines [startLine..endLine] — for inlining into
+     * a trace, capped (lines + chars) so the whole path stays path-scoped even on
+     * a 7-hop chain. Dedents to the body's own indentation and marks truncation.
+     * Shares `cache` with sourceLineAt so each file is read at most once per trace.
+     */
+    private sourceRangeAt;
+    /**
+     * Flow-from-named-symbols: an agent's codegraph_explore query is a bag of
+     * symbol names that usually spans the flow it's investigating (e.g.
+     * "PmsProductController getList PmsProductService list PmsProductServiceImpl").
+     * Surface the longest call chain AMONG those named symbols — scoped to what the
+     * agent explicitly named, so (unlike a fuzzy relevance set) there's no
+     * wrong-feature wandering. Rides synthesized edges, so controller→service-
+     * interface→impl shows up. Returns '' if no chain of >=3 nodes exists.
+     *
+     * Ambiguous tokens (Java `list` → dozens of nodes) are disambiguated by
+     * CO-NAMING: the agent names the class too, so we keep only `list` candidates
+     * whose qualifiedName contains another named token (`PmsProductServiceImpl::list`),
+     * dropping unrelated `OmsOrderService::list`.
+     */
+    private buildFlowFromNamedSymbols;
     /**
      * Handle codegraph_explore — deep exploration in a single call
      *
@@ -180,6 +249,16 @@ export declare class ToolHandler {
      * Handle codegraph_node
      */
     private handleNode;
+    /**
+     * Build the "trail" for a symbol: its direct callees (what it calls) and
+     * callers (what calls it), each with file:line — so codegraph_node doubles as
+     * the structural Grep→Read→expand primitive: a spot PLUS where to go next.
+     * Capped to stay cheap. Walk the graph by calling codegraph_node on a trail
+     * entry; no Read needed for covered hops. Empty edges on a non-leaf often mean
+     * dynamic dispatch the static graph couldn't resolve — that absence is itself
+     * a signal (read that one hop) rather than a dead end.
+     */
+    private formatTrail;
     /**
      * Handle codegraph_status
      */

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

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