@vizalice/codegraph 1.5.0 → 1.6.1

package/dist/installer/targets/codex.js

@@ -2,15 +2,29 @@
 /**
  * OpenAI Codex CLI target.
  *
- *   - MCP server entry to `~/.codex/config.toml` as the dotted-key
- *     table `[mcp_servers.codegraph]`. TOML — not JSON — handled by
- *     the narrow serializer in `./toml.ts`.
- *   - Instructions to `~/.codex/AGENTS.md`.
+ *   - MCP server entry to `config.toml` as the dotted-key table
+ *     `[mcp_servers.codegraph]`. TOML — not JSON — handled by the
+ *     narrow serializer in `./toml.ts`.
+ *   - Instructions to `AGENTS.md`.
  *
- * Codex CLI as of 2026-05 has no project-local config concept —
- * everything lives under `~/.codex/`. `supportsLocation('local')`
- * returns false; the orchestrator skips Codex when the user picks
- * the local install location.
+ * Both locations are supported (#1531):
+ *   - global: `~/.codex/config.toml` + `~/.codex/AGENTS.md`
+ *   - local:  `<cwd>/.codex/config.toml` + `<cwd>/AGENTS.md`
+ *
+ * Codex has a first-class project config layer: `.codex/config.toml`
+ * is layer 4 of the loader's stack, above the user config (layer 6),
+ * merged recursively top-over-bottom
+ * (`codex-rs/config/src/loader/README.md` in openai/codex). It landed
+ * in openai/codex#8354 (2025-12-22), so the "Codex has no
+ * project-local config" note this file used to carry was never
+ * accurate. The project layer strips a denylist of settings that
+ * repo contents shouldn't get to choose (base URLs, model providers,
+ * `notify`, profiles, otel — `loader/mod.rs`), and `mcp_servers` is
+ * NOT on it, so a project-scoped `[mcp_servers.codegraph]` is honored.
+ *
+ * Caveat surfaced as an install note: project layers are "loaded but
+ * disabled when untrusted," so a local install only takes effect in a
+ * project the user has marked trusted.
  *
  * No permissions concept.
  */
@@ -56,27 +70,40 @@ const shared_1 = require("./shared");
 const instructions_template_1 = require("../instructions-template");
 const toml_1 = require("./toml");
 const TOML_HEADER = 'mcp_servers.codegraph';
-function configDir() {
-    return path.join(os.homedir(), '.codex');
+function configDir(loc) {
+    return loc === 'global'
+        ? path.join(os.homedir(), '.codex')
+        : path.join(process.cwd(), '.codex');
+}
+function tomlConfigPath(loc) {
+    return path.join(configDir(loc), 'config.toml');
 }
-function tomlConfigPath() {
-    return path.join(configDir(), 'config.toml');
+function instructionsPath(loc) {
+    // Global AGENTS.md lives under ~/.codex/; project-local AGENTS.md
+    // lives at the project root (NOT under .codex/) — that's the file
+    // Codex reads for repo instructions, and it matches the local
+    // layout the opencode and gemini targets already use.
+    return loc === 'global'
+        ? path.join(configDir('global'), 'AGENTS.md')
+        : path.join(process.cwd(), 'AGENTS.md');
 }
-function instructionsPath() {
-    return path.join(configDir(), 'AGENTS.md');
+/**
+ * Project layers are "loaded but disabled when untrusted" (openai/codex
+ * `loader/mod.rs`), so a local install can be written correctly and
+ * still do nothing. Say so rather than reporting silent success.
+ */
+function trustNote() {
+    return `Codex applies ${tomlConfigPath('local')} only in a project marked trusted — otherwise the layer is loaded but disabled. Trust this project in Codex to activate it.`;
 }
 class CodexTarget {
     id = 'codex';
     displayName = 'Codex CLI';
     docsUrl = 'https://github.com/openai/codex';
-    supportsLocation(loc) {
-        return loc === 'global';
+    supportsLocation(_loc) {
+        return true;
     }
     detect(loc) {
-        if (loc !== 'global') {
-            return { installed: false, alreadyConfigured: false };
-        }
-        const tomlPath = tomlConfigPath();
+        const tomlPath = tomlConfigPath(loc);
         let alreadyConfigured = false;
         if (fs.existsSync(tomlPath)) {
             try {
@@ -85,29 +112,24 @@ class CodexTarget {
             }
             catch { /* ignore */ }
         }
-        const installed = fs.existsSync(configDir());
+        // Global: ~/.codex/ existing means Codex has run here. Local: the
+        // project only counts as "Codex-enabled" once it actually has a
+        // .codex/ dir or config file of its own.
+        const installed = fs.existsSync(configDir(loc)) || fs.existsSync(tomlPath);
         return { installed, alreadyConfigured, configPath: tomlPath };
     }
     install(loc, _opts) {
-        if (loc !== 'global') {
-            return {
-                files: [],
-                notes: ['Codex CLI has no project-local config — re-run with --location=global to install.'],
-            };
-        }
         const files = [];
-        files.push(writeMcpEntry());
+        files.push(writeMcpEntry(loc));
         // AGENTS.md gets the short marker-fenced CodeGraph block (#704):
         // subagents and non-MCP harnesses read AGENTS.md but never the MCP
         // initialize instructions. Upsert self-heals a stale pre-#529 block.
-        files.push((0, shared_1.upsertInstructionsEntry)(instructionsPath()));
-        return { files };
+        files.push((0, shared_1.upsertInstructionsEntry)(instructionsPath(loc)));
+        return loc === 'local' ? { files, notes: [trustNote()] } : { files };
     }
     uninstall(loc) {
-        if (loc !== 'global')
-            return { files: [] };
         const files = [];
-        const tomlPath = tomlConfigPath();
+        const tomlPath = tomlConfigPath(loc);
         if (fs.existsSync(tomlPath)) {
             const content = fs.readFileSync(tomlPath, 'utf-8');
             const { content: nextContent, action } = (0, toml_1.removeTomlTable)(content, TOML_HEADER);
@@ -130,20 +152,15 @@ class CodexTarget {
         else {
             files.push({ path: tomlPath, action: 'not-found' });
         }
-        files.push(removeInstructionsEntry());
+        files.push(removeInstructionsEntry(loc));
         return { files };
     }
     printConfig(loc) {
-        if (loc !== 'global') {
-            return '# Codex CLI has no project-local config — use --location=global.\n';
-        }
         const block = buildCodegraphBlock();
-        return `# Add to ${tomlConfigPath()}\n\n${block}\n`;
+        return `# Add to ${tomlConfigPath(loc)}\n\n${block}\n`;
     }
     describePaths(loc) {
-        if (loc !== 'global')
-            return [];
-        return [tomlConfigPath(), instructionsPath()];
+        return [tomlConfigPath(loc), instructionsPath(loc)];
     }
 }
 function buildCodegraphBlock() {
@@ -153,8 +170,8 @@ function buildCodegraphBlock() {
         args: mcp.args,
     });
 }
-function writeMcpEntry() {
-    const file = tomlConfigPath();
+function writeMcpEntry(loc) {
+    const file = tomlConfigPath(loc);
     const dir = path.dirname(file);
     if (!fs.existsSync(dir))
         fs.mkdirSync(dir, { recursive: true });
@@ -172,12 +189,12 @@ function writeMcpEntry() {
     return { path: file, action: created ? 'created' : 'updated' };
 }
 /**
- * Strip the marker-delimited CodeGraph block from `~/.codex/AGENTS.md`
- * if a prior install wrote one. Used by both install (self-heal on
- * upgrade) and uninstall — see issue #529.
+ * Strip the marker-delimited CodeGraph block from this location's
+ * AGENTS.md if a prior install wrote one. Used by both install
+ * (self-heal on upgrade) and uninstall — see issue #529.
  */
-function removeInstructionsEntry() {
-    const file = instructionsPath();
+function removeInstructionsEntry(loc) {
+    const file = instructionsPath(loc);
     const action = (0, shared_1.removeMarkedSection)(file, instructions_template_1.CODEGRAPH_SECTION_START, instructions_template_1.CODEGRAPH_SECTION_END);
     return { path: file, action };
 }

package/dist/installer/targets/codex.js.map

@@ -1 +1 @@
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package/dist/installer/targets/types.d.ts

@@ -82,10 +82,10 @@ export interface AgentTarget {
     /**
      * Whether this target supports the given install location.
      *
-     * Some agents (Codex CLI as of 2026-05) have no project-local
-     * config concept — only a single `~/.codex/` dir. Returning false
-     * for an unsupported (target, location) pair lets the orchestrator
-     * skip cleanly with a clear message.
+     * Some agents (GitHub Copilot CLI, the Copilot JetBrains plugin)
+     * have no project-local config concept — only a single per-user
+     * config dir. Returning false for an unsupported (target, location)
+     * pair lets the orchestrator skip cleanly with a clear message.
      */
     supportsLocation(loc: Location): boolean;
     detect(loc: Location): DetectionResult;

package/dist/mcp/daemon-manager.d.ts

@@ -16,7 +16,7 @@ export declare function formatUptime(ms: number): string;
  */
 export declare function buildPickItems(daemons: DaemonRecord[], cwdRoot: string | null, now: number): PickItem[];
 export interface PickerDeps {
-    list: () => DaemonRecord[];
+    list: () => DaemonRecord[] | Promise<DaemonRecord[]>;
     stop: (root: string) => Promise<StopResult>;
     stopAll: () => Promise<StopResult[]>;
     /** Realpath'd root of the current project's daemon, or null. */

package/dist/mcp/daemon-manager.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"daemon-manager.d.ts","sourceRoot":"","sources":["../../src/mcp/daemon-manager.ts"],"names":[],"mappings":"AASA,OAAO,KAAK,EAAE,YAAY,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AAElE,0FAA0F;AAC1F,eAAO,MAAM,QAAQ,iBAAiB,CAAC;AACvC,eAAO,MAAM,MAAM,eAAe,CAAC;AAEnC,MAAM,WAAW,QAAQ;IACvB,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,6CAA6C;AAC7C,wBAAgB,YAAY,CAAC,EAAE,EAAE,MAAM,GAAG,MAAM,CAO/C;AAED;;;;GAIG;AACH,wBAAgB,cAAc,CAAC,OAAO,EAAE,YAAY,EAAE,EAAE,OAAO,EAAE,MAAM,GAAG,IAAI,EAAE,GAAG,EAAE,MAAM,GAAG,QAAQ,EAAE,CAwBvG;AAED,MAAM,WAAW,UAAU;IACzB,IAAI,EAAE,MAAM,YAAY,EAAE,GAAG,OAAO,CAAC,YAAY,EAAE,CAAC,CAAC;IACrD,IAAI,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,UAAU,CAAC,CAAC;IAC5C,OAAO,EAAE,MAAM,OAAO,CAAC,UAAU,EAAE,CAAC,CAAC;IACrC,gEAAgE;IAChE,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;IACvB,GAAG,EAAE,MAAM,MAAM,CAAC;IAClB,wEAAwE;IACxE,MAAM,EAAE,CAAC,IAAI,EAAE;QAAE,OAAO,EAAE,MAAM,CAAC;QAAC,OAAO,EAAE,QAAQ,EAAE,CAAC;QAAC,YAAY,EAAE,MAAM,CAAA;KAAE,KAAK,OAAO,CAAC,OAAO,CAAC,CAAC;IACnG,QAAQ,EAAE,CAAC,CAAC,EAAE,OAAO,KAAK,OAAO,CAAC;IAClC,iDAAiD;IACjD,IAAI,EAAE,CAAC,GAAG,EAAE,MAAM,KAAK,IAAI,CAAC;IAC5B,2CAA2C;IAC3C,IAAI,EAAE,CAAC,GAAG,EAAE,MAAM,KAAK,IAAI,CAAC;CAC7B;AAED;;;GAGG;AACH,wBAAsB,eAAe,CAAC,IAAI,EAAE,UAAU,GAAG,OAAO,CAAC,IAAI,CAAC,CAkCrE"}

package/dist/mcp/daemon-manager.js

@@ -97,7 +97,7 @@ function buildPickItems(daemons, cwdRoot, now) {
  */
 async function runDaemonPicker(deps) {
     for (;;) {
-        const daemons = deps.list();
+        const daemons = await deps.list();
         if (daemons.length === 0) {
             deps.done('All daemons stopped.');
             return;

package/dist/mcp/daemon-manager.js.map

@@ -1 +1 @@
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+{"version":3,"file":"daemon-manager.js","sourceRoot":"","sources":["../../src/mcp/daemon-manager.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAsBA,oCAOC;AAOD,wCAwBC;AAsBD,0CAkCC;AApHD;;;;;;;GAOG;AACH,2CAA6B;AAG7B,0FAA0F;AAC7E,QAAA,QAAQ,GAAG,cAAc,CAAC;AAC1B,QAAA,MAAM,GAAG,YAAY,CAAC;AAQnC,6CAA6C;AAC7C,SAAgB,YAAY,CAAC,EAAU;IACrC,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC;IAC7C,IAAI,CAAC,GAAG,EAAE;QAAE,OAAO,GAAG,CAAC,GAAG,CAAC;IAC3B,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC;IAC7B,IAAI,CAAC,GAAG,EAAE;QAAE,OAAO,GAAG,CAAC,GAAG,CAAC;IAC3B,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC;IAC7B,OAAO,GAAG,CAAC,KAAK,CAAC,GAAG,EAAE,GAAG,CAAC;AAC5B,CAAC;AAED;;;;GAIG;AACH,SAAgB,cAAc,CAAC,OAAuB,EAAE,OAAsB,EAAE,GAAW;IACzF,MAAM,GAAG,GAAG,OAAO,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IAC3D,MAAM,OAAO,GAAG,CAAC,GAAG,OAAO,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;QACzC,IAAI,GAAG,EAAE,CAAC;YACR,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC;YAC1C,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC;YAC1C,IAAI,IAAI,IAAI,CAAC,IAAI;gBAAE,OAAO,CAAC,CAAC,CAAC;YAC7B,IAAI,IAAI,IAAI,CAAC,IAAI;gBAAE,OAAO,CAAC,CAAC;QAC9B,CAAC;QACD,OAAO,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,SAAS,CAAC,CAAC,eAAe;IACnD,CAAC,CAAC,CAAC;IAEH,MAAM,KAAK,GAAe,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE;QAC1C,MAAM,OAAO,GAAG,GAAG,IAAI,IAAI,IAAI,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC;QAC5D,OAAO;YACL,KAAK,EAAE,CAAC,CAAC,IAAI;YACb,KAAK,EAAE,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,IAAI,qBAAqB,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI;YACxD,IAAI,EAAE,OAAO,CAAC,CAAC,GAAG,SAAS,YAAY,CAAC,GAAG,GAAG,CAAC,CAAC,SAAS,CAAC,YAAY;SACvE,CAAC;IACJ,CAAC,CAAC,CAAC;IAEH,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC;QAAE,KAAK,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,gBAAQ,EAAE,KAAK,EAAE,UAAU,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC;IACnF,KAAK,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,cAAM,EAAE,KAAK,EAAE,QAAQ,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC;IACzD,OAAO,KAAK,CAAC;AACf,CAAC;AAkBD;;;GAGG;AACI,KAAK,UAAU,eAAe,CAAC,IAAgB;IACpD,SAAS,CAAC;QACR,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,IAAI,EAAE,CAAC;QAClC,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACzB,IAAI,CAAC,IAAI,CAAC,sBAAsB,CAAC,CAAC;YAClC,OAAO;QACT,CAAC;QAED,MAAM,KAAK,GAAG,cAAc,CAAC,OAAO,EAAE,IAAI,CAAC,OAAO,EAAE,IAAI,CAAC,GAAG,EAAE,CAAC,CAAC;QAChE,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC;YAC/B,OAAO,EAAE,yBAAyB;YAClC,OAAO,EAAE,KAAK;YACd,YAAY,EAAE,KAAK,CAAC,CAAC,CAAC,EAAE,KAAK,IAAI,cAAM,EAAE,mDAAmD;SAC7F,CAAC,CAAC;QAEH,IAAI,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,IAAI,MAAM,KAAK,cAAM,EAAE,CAAC;YAC/C,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;YACxB,OAAO;QACT,CAAC;QAED,IAAI,MAAM,KAAK,gBAAQ,EAAE,CAAC;YACxB,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,OAAO,EAAE,CAAC;YACrC,MAAM,CAAC,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,MAAM,IAAI,CAAC,CAAC,OAAO,KAAK,MAAM,CAAC,CAAC,MAAM,CAAC;YACrF,IAAI,CAAC,IAAI,CAAC,WAAW,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC;YACvD,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;YACnB,OAAO;QACT,CAAC;QAED,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;QAC/C,MAAM,MAAM,GAAG,MAAM,CAAC,OAAO,KAAK,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;QAC3D,IAAI,CAAC,IAAI,CAAC,uBAAuB,MAAM,CAAC,GAAG,GAAG,MAAM,OAAO,MAAM,EAAE,CAAC,CAAC;QACrE,6EAA6E;QAC7E,4DAA4D;IAC9D,CAAC;AACH,CAAC"}

package/dist/mcp/daemon-paths.d.ts

@@ -59,6 +59,12 @@ export interface DaemonLockInfo {
     socketPath: string;
     startedAt: number;
 }
+/**
+ * Verify that the process named by a lockfile is the CodeGraph daemon serving
+ * its socket. A bare PID liveness probe is insufficient because OSes reuse PIDs
+ * after an OOM/SIGKILL (#1553).
+ */
+export declare function probeDaemonIdentity(info: DaemonLockInfo, timeoutMs?: number): Promise<boolean>;
 /**
  * Serialize a {@link DaemonLockInfo} for writing to the pidfile. JSON for
  * human readability — operators occasionally `cat` this when debugging.

package/dist/mcp/daemon-paths.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"daemon-paths.d.ts","sourceRoot":"","sources":["../../src/mcp/daemon-paths.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4BG;AA0BH;;;;;;;;;;;;;GAaG;AACH,wBAAgB,yBAAyB,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,EAAE,CAQvE;AAED;;;;;;GAMG;AACH,wBAAgB,mBAAmB,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,CAG/D;AAED,kEAAkE;AAClE,wBAAgB,gBAAgB,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,CAE5D;AAED,+CAA+C;AAC/C,MAAM,WAAW,cAAc;IAC7B,GAAG,EAAE,MAAM,CAAC;IACZ,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,MAAM,CAAC;IACnB,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;;GAGG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,cAAc,GAAG,MAAM,CAE3D;AAED;;;;GAIG;AACH,wBAAgB,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,cAAc,GAAG,IAAI,CAuBjE"}
+{"version":3,"file":"daemon-paths.d.ts","sourceRoot":"","sources":["../../src/mcp/daemon-paths.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4BG;AA2BH;;;;;;;;;;;;;GAaG;AACH,wBAAgB,yBAAyB,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,EAAE,CAQvE;AAED;;;;;;GAMG;AACH,wBAAgB,mBAAmB,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,CAG/D;AAED,kEAAkE;AAClE,wBAAgB,gBAAgB,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,CAE5D;AAED,+CAA+C;AAC/C,MAAM,WAAW,cAAc;IAC7B,GAAG,EAAE,MAAM,CAAC;IACZ,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,MAAM,CAAC;IACnB,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;;;GAIG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,cAAc,EAAE,SAAS,SAAQ,GAAG,OAAO,CAAC,OAAO,CAAC,CA0C7F;AAED;;;GAGG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,cAAc,GAAG,MAAM,CAE3D;AAED;;;;GAIG;AACH,wBAAgB,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,cAAc,GAAG,IAAI,CAuBjE"}

package/dist/mcp/daemon-paths.js

@@ -65,9 +65,11 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.getDaemonSocketCandidates = getDaemonSocketCandidates;
 exports.getDaemonSocketPath = getDaemonSocketPath;
 exports.getDaemonPidPath = getDaemonPidPath;
+exports.probeDaemonIdentity = probeDaemonIdentity;
 exports.encodeLockInfo = encodeLockInfo;
 exports.decodeLockInfo = decodeLockInfo;
 const crypto = __importStar(require("crypto"));
+const net = __importStar(require("net"));
 const os = __importStar(require("os"));
 const path = __importStar(require("path"));
 const directory_1 = require("../directory");
@@ -126,6 +128,58 @@ function getDaemonSocketPath(projectRoot) {
 function getDaemonPidPath(projectRoot) {
     return path.join((0, directory_1.getCodeGraphDir)(projectRoot), 'daemon.pid');
 }
+/**
+ * Verify that the process named by a lockfile is the CodeGraph daemon serving
+ * its socket. A bare PID liveness probe is insufficient because OSes reuse PIDs
+ * after an OOM/SIGKILL (#1553).
+ */
+function probeDaemonIdentity(info, timeoutMs = 1_000) {
+    if (!Number.isInteger(info.pid) || info.pid <= 0 || !info.socketPath)
+        return Promise.resolve(false);
+    return new Promise((resolve) => {
+        let socket;
+        let buffer = '';
+        let done = false;
+        const finish = (ok) => {
+            if (done)
+                return;
+            done = true;
+            clearTimeout(timer);
+            socket.destroy();
+            resolve(ok);
+        };
+        const timer = setTimeout(() => finish(false), timeoutMs);
+        timer.unref?.();
+        try {
+            socket = net.createConnection(info.socketPath);
+        }
+        catch {
+            clearTimeout(timer);
+            resolve(false);
+            return;
+        }
+        socket.setEncoding('utf8');
+        socket.on('data', (chunk) => {
+            buffer += String(chunk);
+            if (buffer.length > 4096)
+                return finish(false);
+            const newline = buffer.indexOf('\n');
+            if (newline < 0)
+                return;
+            try {
+                const hello = JSON.parse(buffer.slice(0, newline));
+                finish(hello.protocol === 1 &&
+                    hello.pid === info.pid &&
+                    (info.version === 'unknown' || hello.codegraph === info.version));
+            }
+            catch {
+                finish(false);
+            }
+        });
+        socket.on('error', () => finish(false));
+        socket.on('close', () => finish(false));
+    });
+}
 /**
  * Serialize a {@link DaemonLockInfo} for writing to the pidfile. JSON for
  * human readability — operators occasionally `cat` this when debugging.

package/dist/mcp/daemon-paths.js.map

@@ -1 +1 @@
-{"version":3,"file":"daemon-paths.js","sourceRoot":"","sources":["../../src/mcp/daemon-paths.ts"],"names":[],"mappings":";AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4BG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAwCH,8DAQC;AASD,kDAGC;AAGD,4CAEC;AAcD,wCAEC;AAOD,wCAuBC;AA7GD,+CAAiC;AACjC,uCAAyB;AACzB,2CAA6B;AAC7B,4CAA+C;AAE/C,oDAAoD;AACpD,MAAM,uBAAuB,GAAG,GAAG,CAAC;AAEpC,8EAA8E;AAC9E,SAAS,WAAW,CAAC,WAAmB;IACtC,OAAO,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;AAClG,CAAC;AAED;;;;;;GAMG;AACH,SAAS,gBAAgB,CAAC,WAAmB;IAC3C,OAAO,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,MAAM,EAAE,EAAE,aAAa,WAAW,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC;AAC9E,CAAC;AAED;;;;;;;;;;;;;GAaG;AACH,SAAgB,yBAAyB,CAAC,WAAmB;IAC3D,IAAI,OAAO,CAAC,QAAQ,KAAK,OAAO,EAAE,CAAC;QACjC,OAAO,CAAC,0BAA0B,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC;IAChE,CAAC;IACD,MAAM,SAAS,GAAG,IAAI,CAAC,IAAI,CAAC,IAAA,2BAAe,EAAC,WAAW,CAAC,EAAE,aAAa,CAAC,CAAC;IACzE,MAAM,GAAG,GAAG,gBAAgB,CAAC,WAAW,CAAC,CAAC;IAC1C,IAAI,SAAS,CAAC,MAAM,GAAG,uBAAuB;QAAE,OAAO,CAAC,GAAG,CAAC,CAAC;IAC7D,OAAO,CAAC,SAAS,EAAE,GAAG,CAAC,CAAC;AAC1B,CAAC;AAED;;;;;;GAMG;AACH,SAAgB,mBAAmB,CAAC,WAAmB;IACrD,4EAA4E;IAC5E,OAAO,yBAAyB,CAAC,WAAW,CAAC,CAAC,CAAC,CAAE,CAAC;AACpD,CAAC;AAED,kEAAkE;AAClE,SAAgB,gBAAgB,CAAC,WAAmB;IAClD,OAAO,IAAI,CAAC,IAAI,CAAC,IAAA,2BAAe,EAAC,WAAW,CAAC,EAAE,YAAY,CAAC,CAAC;AAC/D,CAAC;AAUD;;;GAGG;AACH,SAAgB,cAAc,CAAC,IAAoB;IACjD,OAAO,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,GAAG,IAAI,CAAC;AAC9C,CAAC;AAED;;;;GAIG;AACH,SAAgB,cAAc,CAAC,GAAW;IACxC,MAAM,OAAO,GAAG,GAAG,CAAC,IAAI,EAAE,CAAC;IAC3B,IAAI,CAAC,OAAO;QAAE,OAAO,IAAI,CAAC;IAC1B,IAAI,CAAC;QACH,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;QACnC,IACE,MAAM;YACN,OAAO,MAAM,CAAC,GAAG,KAAK,QAAQ;YAC9B,OAAO,MAAM,CAAC,OAAO,KAAK,QAAQ;YAClC,OAAO,MAAM,CAAC,UAAU,KAAK,QAAQ;YACrC,OAAO,MAAM,CAAC,SAAS,KAAK,QAAQ,EACpC,CAAC;YACD,OAAO,MAAwB,CAAC;QAClC,CAAC;QACD,OAAO,IAAI,CAAC;IACd,CAAC;IAAC,MAAM,CAAC;QACP,6CAA6C;IAC/C,CAAC;IACD,MAAM,GAAG,GAAG,MAAM,CAAC,OAAO,CAAC,CAAC;IAC5B,IAAI,MAAM,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;QACpC,OAAO,EAAE,GAAG,EAAE,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,EAAE,EAAE,SAAS,EAAE,CAAC,EAAE,CAAC;IACnE,CAAC;IACD,OAAO,IAAI,CAAC;AACd,CAAC"}
+{"version":3,"file":"daemon-paths.js","sourceRoot":"","sources":["../../src/mcp/daemon-paths.ts"],"names":[],"mappings":";AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4BG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAyCH,8DAQC;AASD,kDAGC;AAGD,4CAEC;AAeD,kDA0CC;AAMD,wCAEC;AAOD,wCAuBC;AA/JD,+CAAiC;AACjC,yCAA2B;AAC3B,uCAAyB;AACzB,2CAA6B;AAC7B,4CAA+C;AAE/C,oDAAoD;AACpD,MAAM,uBAAuB,GAAG,GAAG,CAAC;AAEpC,8EAA8E;AAC9E,SAAS,WAAW,CAAC,WAAmB;IACtC,OAAO,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;AAClG,CAAC;AAED;;;;;;GAMG;AACH,SAAS,gBAAgB,CAAC,WAAmB;IAC3C,OAAO,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,MAAM,EAAE,EAAE,aAAa,WAAW,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC;AAC9E,CAAC;AAED;;;;;;;;;;;;;GAaG;AACH,SAAgB,yBAAyB,CAAC,WAAmB;IAC3D,IAAI,OAAO,CAAC,QAAQ,KAAK,OAAO,EAAE,CAAC;QACjC,OAAO,CAAC,0BAA0B,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC;IAChE,CAAC;IACD,MAAM,SAAS,GAAG,IAAI,CAAC,IAAI,CAAC,IAAA,2BAAe,EAAC,WAAW,CAAC,EAAE,aAAa,CAAC,CAAC;IACzE,MAAM,GAAG,GAAG,gBAAgB,CAAC,WAAW,CAAC,CAAC;IAC1C,IAAI,SAAS,CAAC,MAAM,GAAG,uBAAuB;QAAE,OAAO,CAAC,GAAG,CAAC,CAAC;IAC7D,OAAO,CAAC,SAAS,EAAE,GAAG,CAAC,CAAC;AAC1B,CAAC;AAED;;;;;;GAMG;AACH,SAAgB,mBAAmB,CAAC,WAAmB;IACrD,4EAA4E;IAC5E,OAAO,yBAAyB,CAAC,WAAW,CAAC,CAAC,CAAC,CAAE,CAAC;AACpD,CAAC;AAED,kEAAkE;AAClE,SAAgB,gBAAgB,CAAC,WAAmB;IAClD,OAAO,IAAI,CAAC,IAAI,CAAC,IAAA,2BAAe,EAAC,WAAW,CAAC,EAAE,YAAY,CAAC,CAAC;AAC/D,CAAC;AAUD;;;;GAIG;AACH,SAAgB,mBAAmB,CAAC,IAAoB,EAAE,SAAS,GAAG,KAAK;IACzE,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,IAAI,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU;QAAE,OAAO,OAAO,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC;IACpG,OAAO,IAAI,OAAO,CAAU,CAAC,OAAO,EAAE,EAAE;QACtC,IAAI,MAAkB,CAAC;QACvB,IAAI,MAAM,GAAG,EAAE,CAAC;QAChB,IAAI,IAAI,GAAG,KAAK,CAAC;QACjB,MAAM,MAAM,GAAG,CAAC,EAAW,EAAE,EAAE;YAC7B,IAAI,IAAI;gBAAE,OAAO;YACjB,IAAI,GAAG,IAAI,CAAC;YACZ,YAAY,CAAC,KAAK,CAAC,CAAC;YACpB,MAAM,CAAC,OAAO,EAAE,CAAC;YACjB,OAAO,CAAC,EAAE,CAAC,CAAC;QACd,CAAC,CAAC;QACF,MAAM,KAAK,GAAG,UAAU,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,EAAE,SAAS,CAAC,CAAC;QACzD,KAAK,CAAC,KAAK,EAAE,EAAE,CAAC;QAChB,IAAI,CAAC;YACH,MAAM,GAAG,GAAG,CAAC,gBAAgB,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;QACjD,CAAC;QAAC,MAAM,CAAC;YACP,YAAY,CAAC,KAAK,CAAC,CAAC;YACpB,OAAO,CAAC,KAAK,CAAC,CAAC;YACf,OAAO;QACT,CAAC;QACD,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC;QAC3B,MAAM,CAAC,EAAE,CAAC,MAAM,EAAE,CAAC,KAAK,EAAE,EAAE;YAC1B,MAAM,IAAI,MAAM,CAAC,KAAK,CAAC,CAAC;YACxB,IAAI,MAAM,CAAC,MAAM,GAAG,IAAI;gBAAE,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC;YAC/C,MAAM,OAAO,GAAG,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;YACrC,IAAI,OAAO,GAAG,CAAC;gBAAE,OAAO;YACxB,IAAI,CAAC;gBACH,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,OAAO,CAAC,CAA4B,CAAC;gBAC9E,MAAM,CACJ,KAAK,CAAC,QAAQ,KAAK,CAAC;oBACpB,KAAK,CAAC,GAAG,KAAK,IAAI,CAAC,GAAG;oBACtB,CAAC,IAAI,CAAC,OAAO,KAAK,SAAS,IAAI,KAAK,CAAC,SAAS,KAAK,IAAI,CAAC,OAAO,CAAC,CACjE,CAAC;YACJ,CAAC;YAAC,MAAM,CAAC;gBACP,MAAM,CAAC,KAAK,CAAC,CAAC;YAChB,CAAC;QACH,CAAC,CAAC,CAAC;QACH,MAAM,CAAC,EAAE,CAAC,OAAO,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC;QACxC,MAAM,CAAC,EAAE,CAAC,OAAO,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC;IAC1C,CAAC,CAAC,CAAC;AACL,CAAC;AAED;;;GAGG;AACH,SAAgB,cAAc,CAAC,IAAoB;IACjD,OAAO,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,GAAG,IAAI,CAAC;AAC9C,CAAC;AAED;;;;GAIG;AACH,SAAgB,cAAc,CAAC,GAAW;IACxC,MAAM,OAAO,GAAG,GAAG,CAAC,IAAI,EAAE,CAAC;IAC3B,IAAI,CAAC,OAAO;QAAE,OAAO,IAAI,CAAC;IAC1B,IAAI,CAAC;QACH,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;QACnC,IACE,MAAM;YACN,OAAO,MAAM,CAAC,GAAG,KAAK,QAAQ;YAC9B,OAAO,MAAM,CAAC,OAAO,KAAK,QAAQ;YAClC,OAAO,MAAM,CAAC,UAAU,KAAK,QAAQ;YACrC,OAAO,MAAM,CAAC,SAAS,KAAK,QAAQ,EACpC,CAAC;YACD,OAAO,MAAwB,CAAC;QAClC,CAAC;QACD,OAAO,IAAI,CAAC;IACd,CAAC;IAAC,MAAM,CAAC;QACP,6CAA6C;IAC/C,CAAC;IACD,MAAM,GAAG,GAAG,MAAM,CAAC,OAAO,CAAC,CAAC;IAC5B,IAAI,MAAM,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;QACpC,OAAO,EAAE,GAAG,EAAE,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,EAAE,EAAE,SAAS,EAAE,CAAC,EAAE,CAAC;IACnE,CAAC;IACD,OAAO,IAAI,CAAC;AACd,CAAC"}

package/dist/mcp/daemon-registry.d.ts

@@ -29,6 +29,16 @@ export declare function deregisterDaemon(root: string): void;
 export declare function listDaemons(opts?: {
     prune?: boolean;
 }): DaemonRecord[];
+/**
+ * Registry entries whose socket hello proves the recorded process is the
+ * daemon. Used by every user-facing list/stop-all path so a reused PID cannot
+ * appear as a phantom running daemon (#1553).
+ */
+export declare function listVerifiedDaemons(opts?: {
+    prune?: boolean;
+}): Promise<DaemonRecord[]>;
+/** Remove daemon artifacts only when no matching daemon answers the socket hello. */
+export declare function clearStaleDaemonArtifacts(root: string): Promise<boolean>;
 export interface StopResult {
     root: string;
     pid: number | null;

package/dist/mcp/daemon-registry.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"daemon-registry.d.ts","sourceRoot":"","sources":["../../src/mcp/daemon-registry.ts"],"names":[],"mappings":"AA0BA,MAAM,WAAW,YAAY;IAC3B,iDAAiD;IACjD,IAAI,EAAE,MAAM,CAAC;IACb,GAAG,EAAE,MAAM,CAAC;IACZ,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,MAAM,CAAC;IACnB,iDAAiD;IACjD,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;;GAGG;AACH,wBAAgB,cAAc,IAAI,MAAM,CAEvC;AAOD;;;;GAIG;AACH,wBAAgB,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAQnD;AAED,0EAA0E;AAC1E,wBAAgB,cAAc,CAAC,GAAG,EAAE,YAAY,GAAG,IAAI,CAOtD;AAED,mEAAmE;AACnE,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI,CAMnD;AAED;;;GAGG;AACH,wBAAgB,WAAW,CAAC,IAAI,GAAE;IAAE,KAAK,CAAC,EAAE,OAAO,CAAA;CAAO,GAAG,YAAY,EAAE,CA2B1E;AA2BD,MAAM,WAAW,UAAU;IACzB,IAAI,EAAE,MAAM,CAAC;IACb,GAAG,EAAE,MAAM,GAAG,IAAI,CAAC;IACnB,uFAAuF;IACvF,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,aAAa,GAAG,WAAW,CAAC;CACxD;AAED;;;;;GAKG;AACH,wBAAsB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,UAAU,CAAC,CAmCpE;AAED,0CAA0C;AAC1C,wBAAsB,cAAc,IAAI,OAAO,CAAC,UAAU,EAAE,CAAC,CAM5D"}
+{"version":3,"file":"daemon-registry.d.ts","sourceRoot":"","sources":["../../src/mcp/daemon-registry.ts"],"names":[],"mappings":"AAgCA,MAAM,WAAW,YAAY;IAC3B,iDAAiD;IACjD,IAAI,EAAE,MAAM,CAAC;IACb,GAAG,EAAE,MAAM,CAAC;IACZ,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,MAAM,CAAC;IACnB,iDAAiD;IACjD,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;;GAGG;AACH,wBAAgB,cAAc,IAAI,MAAM,CAEvC;AAOD;;;;GAIG;AACH,wBAAgB,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAQnD;AAED,0EAA0E;AAC1E,wBAAgB,cAAc,CAAC,GAAG,EAAE,YAAY,GAAG,IAAI,CAOtD;AAED,mEAAmE;AACnE,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI,CAMnD;AAED;;;GAGG;AACH,wBAAgB,WAAW,CAAC,IAAI,GAAE;IAAE,KAAK,CAAC,EAAE,OAAO,CAAA;CAAO,GAAG,YAAY,EAAE,CA2B1E;AAED;;;;GAIG;AACH,wBAAsB,mBAAmB,CAAC,IAAI,GAAE;IAAE,KAAK,CAAC,EAAE,OAAO,CAAA;CAAO,GAAG,OAAO,CAAC,YAAY,EAAE,CAAC,CAajG;AAgBD,qFAAqF;AACrF,wBAAsB,yBAAyB,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CAW9E;AAaD,MAAM,WAAW,UAAU;IACzB,IAAI,EAAE,MAAM,CAAC;IACb,GAAG,EAAE,MAAM,GAAG,IAAI,CAAC;IACnB,uFAAuF;IACvF,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,aAAa,GAAG,WAAW,CAAC;CACxD;AAED;;;;;GAKG;AACH,wBAAsB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,UAAU,CAAC,CA2CpE;AAED,0CAA0C;AAC1C,wBAAsB,cAAc,IAAI,OAAO,CAAC,UAAU,EAAE,CAAC,CAM5D"}

package/dist/mcp/daemon-registry.js

@@ -38,6 +38,8 @@ exports.isProcessAlive = isProcessAlive;
 exports.registerDaemon = registerDaemon;
 exports.deregisterDaemon = deregisterDaemon;
 exports.listDaemons = listDaemons;
+exports.listVerifiedDaemons = listVerifiedDaemons;
+exports.clearStaleDaemonArtifacts = clearStaleDaemonArtifacts;
 exports.stopDaemonAt = stopDaemonAt;
 exports.stopAllDaemons = stopAllDaemons;
 /**
@@ -148,6 +150,27 @@ function listDaemons(opts = {}) {
     }
     return live.sort((a, b) => b.startedAt - a.startedAt);
 }
+/**
+ * Registry entries whose socket hello proves the recorded process is the
+ * daemon. Used by every user-facing list/stop-all path so a reused PID cannot
+ * appear as a phantom running daemon (#1553).
+ */
+async function listVerifiedDaemons(opts = {}) {
+    const prune = opts.prune ?? true;
+    const candidates = listDaemons({ prune });
+    const checks = await Promise.all(candidates.map(async (rec) => ({
+        rec,
+        verified: await (0, daemon_paths_1.probeDaemonIdentity)(rec),
+    })));
+    const verified = [];
+    for (const check of checks) {
+        if (check.verified)
+            verified.push(check.rec);
+        else if (prune)
+            deregisterDaemon(check.rec.root);
+    }
+    return verified;
+}
 /** Remove a stopped daemon's leftover lockfile + socket + registry record. */
 function cleanupDaemonArtifacts(root) {
     try {
@@ -167,6 +190,22 @@ function cleanupDaemonArtifacts(root) {
     }
     deregisterDaemon(root);
 }
+/** Remove daemon artifacts only when no matching daemon answers the socket hello. */
+async function clearStaleDaemonArtifacts(root) {
+    const pidPath = (0, daemon_paths_1.getDaemonPidPath)(root);
+    const hadArtifacts = fs.existsSync(pidPath) || (process.platform !== 'win32' && (0, daemon_paths_1.getDaemonSocketCandidates)(root).some((p) => fs.existsSync(p)));
+    if (!hadArtifacts)
+        return false;
+    let info = null;
+    try {
+        info = (0, daemon_paths_1.decodeLockInfo)(fs.readFileSync(pidPath, 'utf8'));
+    }
+    catch { /* missing/corrupt */ }
+    if (info && isProcessAlive(info.pid) && await (0, daemon_paths_1.probeDaemonIdentity)(info))
+        return false;
+    cleanupDaemonArtifacts(root);
+    return true;
+}
 const sleep = (ms) => new Promise((r) => setTimeout(r, ms));
 async function waitForDeath(pid, timeoutMs) {
     const deadline = Date.now() + timeoutMs;
@@ -185,9 +224,10 @@ async function waitForDeath(pid, timeoutMs) {
  */
 async function stopDaemonAt(root) {
     let pid = null;
+    let identity = null;
     try {
-        const info = (0, daemon_paths_1.decodeLockInfo)(fs.readFileSync((0, daemon_paths_1.getDaemonPidPath)(root), 'utf8'));
-        pid = info?.pid ?? null;
+        identity = (0, daemon_paths_1.decodeLockInfo)(fs.readFileSync((0, daemon_paths_1.getDaemonPidPath)(root), 'utf8'));
+        pid = identity?.pid ?? null;
     }
     catch {
         /* no lockfile */
@@ -195,6 +235,8 @@ async function stopDaemonAt(root) {
     if (pid == null) {
         const rec = listDaemons({ prune: false }).find((r) => path.resolve(r.root) === path.resolve(root));
         pid = rec?.pid ?? null;
+        if (rec)
+            identity = rec;
     }
     if (pid == null) {
         cleanupDaemonArtifacts(root);
@@ -204,6 +246,12 @@ async function stopDaemonAt(root) {
         cleanupDaemonArtifacts(root);
         return { root, pid, outcome: 'not-running' };
     }
+    // Never signal a process merely because it reused a stale daemon PID. The
+    // daemon's immediate hello is the process-identity proof (#1553).
+    if (!identity || !await (0, daemon_paths_1.probeDaemonIdentity)(identity)) {
+        cleanupDaemonArtifacts(root);
+        return { root, pid, outcome: 'not-running' };
+    }
     // POSIX: SIGTERM runs the daemon's graceful shutdown. Windows: TerminateProcess
     // (no graceful path), so we always sweep artifacts ourselves below.
     try {
@@ -225,7 +273,7 @@ async function stopDaemonAt(root) {
 /** Stop every registered, live daemon. */
 async function stopAllDaemons() {
     const results = [];
-    for (const rec of listDaemons()) {
+    for (const rec of await listVerifiedDaemons()) {
         results.push(await stopDaemonAt(rec.root));
     }
     return results;

package/dist/mcp/daemon-registry.js.map

@@ -1 +1 @@
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package/dist/mcp/daemon.d.ts

@@ -234,17 +234,20 @@ export declare function tryAcquireDaemonLock(projectRoot: string): AcquireResult
  */
 export declare function acquireLockViaExclusiveOpen(pidPath: string, info: DaemonLockInfo): boolean;
 /**
- * Remove a stale pidfile, but only if it still names a dead process. Re-reads
- * the file immediately before unlinking so we never delete a lock that a live
- * daemon (re)acquired in the meantime.
+ * Remove a stale pidfile. Re-reads the file immediately before unlinking so a
+ * different daemon that acquired the lock in the meantime is never disturbed.
  *
  * must-fix 1 (issue #411 review): the original unconditionally `unlink`'d,
  * which let a racing candidate delete a healthy daemon's lock. Passing
  * `expectedDeadPid` (the pid the caller believed was dead) makes the clear a
- * compare-and-delete: bail if the file now holds a different pid, or any live
- * pid. Returns true when the stale lock is gone (or was already gone).
+ * compare-and-delete: bail if the file now holds a different pid. By default a
+ * live pid is also preserved; `allowLivePid` is reserved for callers that have
+ * already disproved daemon identity with the socket hello (#1553). Returns true
+ * when the stale lock is gone (or was already gone).
  */
-export declare function clearStaleDaemonLock(pidPath: string, expectedDeadPid?: number): boolean;
+export declare function clearStaleDaemonLock(pidPath: string, expectedDeadPid?: number, opts?: {
+    allowLivePid?: boolean;
+}): boolean;
 /**
  * Probe whether `pid` is currently alive (signal-0). Treats EPERM as alive on
  * every platform (the process exists, it's just not ours to signal) so we never

package/dist/mcp/daemon.d.ts.map

@@ -1 +1 @@
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package/dist/mcp/daemon.js

@@ -616,17 +616,18 @@ function acquireLockViaExclusiveOpen(pidPath, info) {
     return true;
 }
 /**
- * Remove a stale pidfile, but only if it still names a dead process. Re-reads
- * the file immediately before unlinking so we never delete a lock that a live
- * daemon (re)acquired in the meantime.
+ * Remove a stale pidfile. Re-reads the file immediately before unlinking so a
+ * different daemon that acquired the lock in the meantime is never disturbed.
  *
  * must-fix 1 (issue #411 review): the original unconditionally `unlink`'d,
  * which let a racing candidate delete a healthy daemon's lock. Passing
  * `expectedDeadPid` (the pid the caller believed was dead) makes the clear a
- * compare-and-delete: bail if the file now holds a different pid, or any live
- * pid. Returns true when the stale lock is gone (or was already gone).
+ * compare-and-delete: bail if the file now holds a different pid. By default a
+ * live pid is also preserved; `allowLivePid` is reserved for callers that have
+ * already disproved daemon identity with the socket hello (#1553). Returns true
+ * when the stale lock is gone (or was already gone).
  */
-function clearStaleDaemonLock(pidPath, expectedDeadPid) {
+function clearStaleDaemonLock(pidPath, expectedDeadPid, opts = {}) {
     try {
         const raw = fs.readFileSync(pidPath, 'utf8');
         const info = (0, daemon_paths_1.decodeLockInfo)(raw);
@@ -634,8 +635,9 @@ function clearStaleDaemonLock(pidPath, expectedDeadPid) {
             // A different pid took over since we read it — not ours to clear.
             if (expectedDeadPid !== undefined && info.pid !== expectedDeadPid)
                 return false;
-            // Holder is actually alive — never clear a live daemon's lock.
-            if (info.pid > 0 && isProcessAlive(info.pid))
+            // PID liveness is normally sufficient. The takeover caller may override
+            // it only after a failed identity handshake proves PID reuse.
+            if (!opts.allowLivePid && info.pid > 0 && isProcessAlive(info.pid))
                 return false;
         }
         fs.unlinkSync(pidPath);