@colbymchenry/codegraph-darwin-x64 1.0.1 → 1.1.0

package/lib/dist/installer/targets/claude.js

@@ -54,7 +54,9 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.claudeTarget = void 0;
 exports.writeMcpEntry = writeMcpEntry;
 exports.cleanupLegacyHooks = cleanupLegacyHooks;
+exports.removePromptHookEntry = removePromptHookEntry;
 exports.writePermissionsEntry = writePermissionsEntry;
+exports.writePromptHookEntry = writePromptHookEntry;
 exports.removeInstructionsEntry = removeInstructionsEntry;
 const fs = __importStar(require("fs"));
 const path = __importStar(require("path"));
@@ -134,6 +136,19 @@ class ClaudeCodeTarget {
         const hookCleanup = cleanupLegacyHooks(loc);
         if (hookCleanup.action === 'removed')
             files.push(hookCleanup);
+        // 2c. Front-load prompt hook (Claude UserPromptSubmit). Opt-in via the
+        // installer prompt (default-yes): `promptHook === true` writes it;
+        // `=== false` strips any a prior install wrote so opting out round-trips
+        // (and an upgrade re-run honors the new choice); `undefined` leaves it
+        // untouched for callers that don't manage it.
+        if (opts.promptHook === true) {
+            files.push(writePromptHookEntry(loc));
+        }
+        else if (opts.promptHook === false) {
+            const removed = removePromptHookEntry(loc);
+            if (removed.action === 'removed')
+                files.push(removed);
+        }
         // 3. CLAUDE.md instructions — the short marker-fenced CodeGraph
         // block (#704). The MCP initialize instructions reach only the main
         // agent; CLAUDE.md is what Task-tool subagents (and non-MCP
@@ -196,6 +211,10 @@ class ClaudeCodeTarget {
         const hookCleanup = cleanupLegacyHooks(loc);
         if (hookCleanup.action === 'removed')
             files.push(hookCleanup);
+        // 2c. Remove the front-load prompt hook this installer may have written.
+        const promptHookCleanup = removePromptHookEntry(loc);
+        if (promptHookCleanup.action === 'removed')
+            files.push(promptHookCleanup);
         // 3. Instructions — strip the legacy CodeGraph block if present.
         files.push(removeInstructionsEntry(loc));
         return { files };
@@ -286,6 +305,15 @@ function isLegacyCodegraphHookCommand(command) {
     return (command.includes('codegraph mark-dirty') ||
         command.includes('codegraph sync-if-dirty'));
 }
+/**
+ * The front-load prompt-hook command the installer writes into Claude's
+ * `UserPromptSubmit` (see writePromptHookEntry). Matched by substring so an
+ * `npx @colbymchenry/codegraph prompt-hook` form is recognized too.
+ */
+const PROMPT_HOOK_COMMAND = 'codegraph prompt-hook';
+function isPromptHookCommand(command) {
+    return typeof command === 'string' && command.includes(PROMPT_HOOK_COMMAND);
+}
 /**
  * Remove stale codegraph auto-sync hooks from Claude `settings.json`.
  *
@@ -301,7 +329,7 @@ function isLegacyCodegraphHookCommand(command) {
  * Exported so it can be unit-tested directly and reused by both
  * `install` (an upgrade self-heals) and `uninstall`.
  */
-function cleanupLegacyHooks(loc) {
+function removeHookCommandsMatching(loc, match) {
     const file = settingsJsonPath(loc);
     if (!fs.existsSync(file))
         return { path: file, action: 'not-found' };
@@ -310,7 +338,7 @@ function cleanupLegacyHooks(loc) {
     if (!hooks || typeof hooks !== 'object' || Array.isArray(hooks)) {
         return { path: file, action: 'unchanged' };
     }
-    // Pass 1: drop the legacy command(s) from inside every matcher group.
+    // Pass 1: drop matching command(s) from inside every matcher group.
     let removedAny = false;
     for (const event of Object.keys(hooks)) {
         const groups = hooks[event];
@@ -320,16 +348,17 @@ function cleanupLegacyHooks(loc) {
             if (!group || !Array.isArray(group.hooks))
                 continue;
             const before = group.hooks.length;
-            group.hooks = group.hooks.filter((h) => !isLegacyCodegraphHookCommand(h?.command));
+            group.hooks = group.hooks.filter((h) => !match(h?.command));
             if (group.hooks.length !== before)
                 removedAny = true;
         }
     }
     if (!removedAny)
         return { path: file, action: 'unchanged' };
-    // Pass 2: prune empty matcher groups, then events with no groups
-    // left, then an empty top-level `hooks`. Guarded by `removedAny` so
-    // we never restructure a settings.json that had no codegraph hooks.
+    // Pass 2: prune empty matcher groups, then events with no groups left,
+    // then an empty top-level `hooks`. Guarded by `removedAny` so we never
+    // restructure a settings.json that had no matching hooks. Sibling hooks
+    // (a different command in the group, or a different event) survive.
     for (const event of Object.keys(hooks)) {
         const groups = hooks[event];
         if (!Array.isArray(groups))
@@ -343,6 +372,22 @@ function cleanupLegacyHooks(loc) {
     (0, shared_1.writeJsonFile)(file, settings);
     return { path: file, action: 'removed' };
 }
+/**
+ * Remove stale codegraph auto-sync hooks (`mark-dirty` / `sync-if-dirty`) that a
+ * pre-0.8 install wrote. Exported for direct unit-testing; reused by both
+ * `install` (an upgrade self-heals) and `uninstall`.
+ */
+function cleanupLegacyHooks(loc) {
+    return removeHookCommandsMatching(loc, isLegacyCodegraphHookCommand);
+}
+/**
+ * Remove the front-load `UserPromptSubmit` hook this installer writes (see
+ * writePromptHookEntry). Used by `uninstall`, and by `install` when the user
+ * opts out, so the choice round-trips.
+ */
+function removePromptHookEntry(loc) {
+    return removeHookCommandsMatching(loc, isPromptHookCommand);
+}
 function writePermissionsEntry(loc) {
     const file = settingsJsonPath(loc);
     const settings = (0, shared_1.readJsonFile)(file);
@@ -364,6 +409,33 @@ function writePermissionsEntry(loc) {
     (0, shared_1.writeJsonFile)(file, settings);
     return { path: file, action: created ? 'created' : 'updated' };
 }
+/**
+ * Write the front-load `UserPromptSubmit` hook into Claude `settings.json` —
+ * a `command` hook that runs `codegraph prompt-hook`, which injects
+ * codegraph_explore context for structural prompts so the agent reliably uses
+ * the graph. Idempotent: if our command is already wired under UserPromptSubmit
+ * the file is left byte-for-byte untouched and reported `unchanged`. Sibling
+ * hooks (the user's own, or other events) are preserved. Opt-in — the installer
+ * only calls this when the user accepts the prompt (default-yes).
+ */
+function writePromptHookEntry(loc) {
+    const file = settingsJsonPath(loc);
+    const created = !fs.existsSync(file);
+    const settings = (0, shared_1.readJsonFile)(file);
+    if (!settings.hooks || typeof settings.hooks !== 'object' || Array.isArray(settings.hooks)) {
+        settings.hooks = {};
+    }
+    if (!Array.isArray(settings.hooks.UserPromptSubmit))
+        settings.hooks.UserPromptSubmit = [];
+    const already = settings.hooks.UserPromptSubmit.some((g) => g && Array.isArray(g.hooks) && g.hooks.some((h) => isPromptHookCommand(h?.command)));
+    if (already)
+        return { path: file, action: 'unchanged' };
+    settings.hooks.UserPromptSubmit.push({
+        hooks: [{ type: 'command', command: PROMPT_HOOK_COMMAND }],
+    });
+    (0, shared_1.writeJsonFile)(file, settings);
+    return { path: file, action: created ? 'created' : 'updated' };
+}
 /**
  * Strip the marker-delimited CodeGraph block from CLAUDE.md if a prior
  * install wrote one. Codegraph no longer maintains an instructions file

package/lib/dist/installer/targets/claude.js.map

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

@@ -19,8 +19,18 @@ export declare function getMcpServerConfig(): {
 };
 /**
  * Permissions list for Claude `settings.json`. Other targets that
- * have a permissions concept can compose this list directly. The
- * permission strings follow Claude's `mcp__<server>__<tool>` format.
+ * have a permissions concept can compose this list directly.
+ *
+ * One server-scoped wildcard rather than a per-tool list. By default only
+ * `codegraph_explore` is even LISTED to the agent (see DEFAULT_MCP_TOOLS in
+ * mcp/tools.ts), so in practice explore is the only tool this auto-approves —
+ * but the wildcard means that if a user re-enables another tool via
+ * CODEGRAPH_MCP_TOOLS, it's already pre-approved (no permission prompt, no
+ * hand-editing settings.json), and future tools are covered too. Claude only
+ * honors globs after a literal `mcp__<server>__` prefix, so this exact string
+ * is the way to allow-all for one server; a bare `mcp__codegraph` or `*` is
+ * ignored. The allowlist gates PROMPTING, not visibility, so a superset here
+ * never makes a hidden tool appear.
  */
 export declare function getCodeGraphPermissions(): string[];
 /**

package/lib/dist/installer/targets/shared.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"shared.d.ts","sourceRoot":"","sources":["../../../src/installer/targets/shared.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAUH;;;;GAIG;AACH,wBAAgB,kBAAkB,IAAI;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,EAAE,CAAA;CAAE,CAMtF;AAED;;;;GAIG;AACH,wBAAgB,uBAAuB,IAAI,MAAM,EAAE,CAWlD;AAED;;;;;;GAMG;AACH,wBAAgB,YAAY,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,CAelE;AAED;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,IAAI,CAa3E;AAED;;;GAGG;AACH,wBAAgB,aAAa,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,GAAG,IAAI,CAE/E;AAED;;;;;;GAMG;AACH,wBAAgB,aAAa,CAAC,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,OAAO,GAAG,OAAO,CAiB7D;AAED;;;;;;;;;;;GAWG;AACH,wBAAgB,4BAA4B,CAC1C,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,EACZ,WAAW,EAAE,MAAM,EACnB,SAAS,EAAE,MAAM,GAChB,SAAS,GAAG,SAAS,GAAG,UAAU,GAAG,WAAW,CA2BlD;AAED;;;;;;;;;GASG;AACH,wBAAgB,uBAAuB,CAAC,IAAI,EAAE,MAAM,GAAG;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,SAAS,GAAG,SAAS,GAAG,WAAW,CAAA;CAAE,CAQnH;AAED;;;;;;;;GAQG;AACH,wBAAgB,mBAAmB,CACjC,QAAQ,EAAE,MAAM,EAChB,WAAW,EAAE,MAAM,EACnB,SAAS,EAAE,MAAM,GAChB,SAAS,GAAG,WAAW,GAAG,MAAM,CAwBlC"}
+{"version":3,"file":"shared.d.ts","sourceRoot":"","sources":["../../../src/installer/targets/shared.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAUH;;;;GAIG;AACH,wBAAgB,kBAAkB,IAAI;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,EAAE,CAAA;CAAE,CAMtF;AAED;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,uBAAuB,IAAI,MAAM,EAAE,CAElD;AAED;;;;;;GAMG;AACH,wBAAgB,YAAY,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,CAelE;AAED;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,IAAI,CAa3E;AAED;;;GAGG;AACH,wBAAgB,aAAa,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,GAAG,IAAI,CAE/E;AAED;;;;;;GAMG;AACH,wBAAgB,aAAa,CAAC,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,OAAO,GAAG,OAAO,CAiB7D;AAED;;;;;;;;;;;GAWG;AACH,wBAAgB,4BAA4B,CAC1C,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,EACZ,WAAW,EAAE,MAAM,EACnB,SAAS,EAAE,MAAM,GAChB,SAAS,GAAG,SAAS,GAAG,UAAU,GAAG,WAAW,CA2BlD;AAED;;;;;;;;;GASG;AACH,wBAAgB,uBAAuB,CAAC,IAAI,EAAE,MAAM,GAAG;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,SAAS,GAAG,SAAS,GAAG,WAAW,CAAA;CAAE,CAQnH;AAED;;;;;;;;GAQG;AACH,wBAAgB,mBAAmB,CACjC,QAAQ,EAAE,MAAM,EAChB,WAAW,EAAE,MAAM,EACnB,SAAS,EAAE,MAAM,GAChB,SAAS,GAAG,WAAW,GAAG,MAAM,CAwBlC"}

package/lib/dist/installer/targets/shared.js

@@ -68,20 +68,21 @@ function getMcpServerConfig() {
 }
 /**
  * Permissions list for Claude `settings.json`. Other targets that
- * have a permissions concept can compose this list directly. The
- * permission strings follow Claude's `mcp__<server>__<tool>` format.
+ * have a permissions concept can compose this list directly.
+ *
+ * One server-scoped wildcard rather than a per-tool list. By default only
+ * `codegraph_explore` is even LISTED to the agent (see DEFAULT_MCP_TOOLS in
+ * mcp/tools.ts), so in practice explore is the only tool this auto-approves —
+ * but the wildcard means that if a user re-enables another tool via
+ * CODEGRAPH_MCP_TOOLS, it's already pre-approved (no permission prompt, no
+ * hand-editing settings.json), and future tools are covered too. Claude only
+ * honors globs after a literal `mcp__<server>__` prefix, so this exact string
+ * is the way to allow-all for one server; a bare `mcp__codegraph` or `*` is
+ * ignored. The allowlist gates PROMPTING, not visibility, so a superset here
+ * never makes a hidden tool appear.
  */
 function getCodeGraphPermissions() {
-    return [
-        'mcp__codegraph__codegraph_explore',
-        'mcp__codegraph__codegraph_search',
-        'mcp__codegraph__codegraph_node',
-        'mcp__codegraph__codegraph_callers',
-        'mcp__codegraph__codegraph_callees',
-        'mcp__codegraph__codegraph_impact',
-        'mcp__codegraph__codegraph_files',
-        'mcp__codegraph__codegraph_status',
-    ];
+    return ['mcp__codegraph__*'];
 }
 /**
  * Read a JSON file, returning `{}` when missing or unparseable.

package/lib/dist/installer/targets/shared.js.map

@@ -1 +1 @@
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+{"version":3,"file":"shared.js","sourceRoot":"","sources":["../../../src/installer/targets/shared.ts"],"names":[],"mappings":";AAAA;;;;;;;;GAQG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAeH,gDAMC;AAiBD,0DAEC;AASD,oCAeC;AAQD,kDAaC;AAMD,sCAEC;AASD,sCAiBC;AAcD,oEAgCC;AAYD,0DAQC;AAWD,kDA4BC;AA9ND,uCAAyB;AACzB,2CAA6B;AAC7B,oEAIkC;AAElC;;;;GAIG;AACH,SAAgB,kBAAkB;IAChC,OAAO;QACL,IAAI,EAAE,OAAO;QACb,OAAO,EAAE,WAAW;QACpB,IAAI,EAAE,CAAC,OAAO,EAAE,OAAO,CAAC;KACzB,CAAC;AACJ,CAAC;AAED;;;;;;;;;;;;;;GAcG;AACH,SAAgB,uBAAuB;IACrC,OAAO,CAAC,mBAAmB,CAAC,CAAC;AAC/B,CAAC;AAED;;;;;;GAMG;AACH,SAAgB,YAAY,CAAC,QAAgB;IAC3C,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,QAAQ,CAAC,EAAE,CAAC;QAC7B,OAAO,EAAE,CAAC;IACZ,CAAC;IACD,IAAI,CAAC;QACH,OAAO,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,YAAY,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC,CAAC;IACxD,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QAC7D,OAAO,CAAC,IAAI,CAAC,8BAA8B,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC,KAAK,GAAG,EAAE,CAAC,CAAC;QAC9E,OAAO,CAAC,IAAI,CAAC,gDAAgD,CAAC,CAAC;QAC/D,IAAI,CAAC;YACH,EAAE,CAAC,YAAY,CAAC,QAAQ,EAAE,QAAQ,GAAG,SAAS,CAAC,CAAC;QAClD,CAAC;QAAC,MAAM,CAAC,CAAC,2BAA2B,CAAC,CAAC;QACvC,OAAO,EAAE,CAAC;IACZ,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACH,SAAgB,mBAAmB,CAAC,QAAgB,EAAE,OAAe;IACnE,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC;IACnC,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;QACxB,EAAE,CAAC,SAAS,CAAC,GAAG,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IACzC,CAAC;IACD,MAAM,OAAO,GAAG,QAAQ,GAAG,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC;IACjD,IAAI,CAAC;QACH,EAAE,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;QACnC,EAAE,CAAC,UAAU,CAAC,OAAO,EAAE,QAAQ,CAAC,CAAC;IACnC,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,IAAI,CAAC;YAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC;QAAC,CAAC;QAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC;QACtD,MAAM,GAAG,CAAC;IACZ,CAAC;AACH,CAAC;AAED;;;GAGG;AACH,SAAgB,aAAa,CAAC,QAAgB,EAAE,IAAyB;IACvE,mBAAmB,CAAC,QAAQ,EAAE,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;AACtE,CAAC;AAED;;;;;;GAMG;AACH,SAAgB,aAAa,CAAC,CAAU,EAAE,CAAU;IAClD,IAAI,CAAC,KAAK,CAAC;QAAE,OAAO,IAAI,CAAC;IACzB,IAAI,OAAO,CAAC,KAAK,OAAO,CAAC;QAAE,OAAO,KAAK,CAAC;IACxC,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,IAAI;QAAE,OAAO,CAAC,KAAK,CAAC,CAAC;IAC7C,IAAI,OAAO,CAAC,KAAK,QAAQ;QAAE,OAAO,KAAK,CAAC;IACxC,IAAI,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QAAE,OAAO,KAAK,CAAC;IACxD,IAAI,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC;QACzC,IAAI,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,MAAM;YAAE,OAAO,KAAK,CAAC;QACxC,OAAO,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,aAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IACnD,CAAC;IACD,MAAM,EAAE,GAAG,CAA4B,CAAC;IACxC,MAAM,EAAE,GAAG,CAA4B,CAAC;IACxC,MAAM,EAAE,GAAG,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;IAClC,MAAM,EAAE,GAAG,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;IAClC,IAAI,EAAE,CAAC,MAAM,KAAK,EAAE,CAAC,MAAM;QAAE,OAAO,KAAK,CAAC;IAC1C,IAAI,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC;QAAE,OAAO,KAAK,CAAC;IACnD,OAAO,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,aAAa,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;AACtD,CAAC;AAED;;;;;;;;;;;GAWG;AACH,SAAgB,4BAA4B,CAC1C,QAAgB,EAChB,IAAY,EACZ,WAAmB,EACnB,SAAiB;IAEjB,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,QAAQ,CAAC,EAAE,CAAC;QAC7B,mBAAmB,CAAC,QAAQ,EAAE,IAAI,GAAG,IAAI,CAAC,CAAC;QAC3C,OAAO,SAAS,CAAC;IACnB,CAAC;IAED,MAAM,OAAO,GAAG,EAAE,CAAC,YAAY,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;IACnD,MAAM,QAAQ,GAAG,OAAO,CAAC,OAAO,CAAC,WAAW,CAAC,CAAC;IAC9C,MAAM,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;IAE1C,IAAI,QAAQ,KAAK,CAAC,CAAC,IAAI,MAAM,GAAG,QAAQ,EAAE,CAAC;QACzC,MAAM,aAAa,GAAG,OAAO,CAAC,SAAS,CAAC,QAAQ,EAAE,MAAM,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC;QAC7E,IAAI,aAAa,KAAK,IAAI,EAAE,CAAC;YAC3B,OAAO,WAAW,CAAC;QACrB,CAAC;QACD,MAAM,MAAM,GAAG,OAAO,CAAC,SAAS,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAC;QAC9C,MAAM,KAAK,GAAG,OAAO,CAAC,SAAS,CAAC,MAAM,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC;QAC3D,mBAAmB,CAAC,QAAQ,EAAE,MAAM,GAAG,IAAI,GAAG,KAAK,CAAC,CAAC;QACrD,OAAO,SAAS,CAAC;IACnB,CAAC;IAED,mEAAmE;IACnE,cAAc;IACd,MAAM,OAAO,GAAG,OAAO,CAAC,OAAO,EAAE,CAAC;IAClC,MAAM,GAAG,GAAG,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC;IAC7C,mBAAmB,CAAC,QAAQ,EAAE,OAAO,GAAG,GAAG,GAAG,IAAI,GAAG,IAAI,CAAC,CAAC;IAC3D,OAAO,UAAU,CAAC;AACpB,CAAC;AAED;;;;;;;;;GASG;AACH,SAAgB,uBAAuB,CAAC,IAAY;IAClD,MAAM,MAAM,GAAG,4BAA4B,CACzC,IAAI,EACJ,oDAA4B,EAC5B,+CAAuB,EACvB,6CAAqB,CACtB,CAAC;IACF,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,MAAM,EAAE,MAAM,KAAK,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;AAC5E,CAAC;AAED;;;;;;;;GAQG;AACH,SAAgB,mBAAmB,CACjC,QAAgB,EAChB,WAAmB,EACnB,SAAiB;IAEjB,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,QAAQ,CAAC;QAAE,OAAO,MAAM,CAAC;IAE5C,IAAI,OAAe,CAAC;IACpB,IAAI,CAAC;QACH,OAAO,GAAG,EAAE,CAAC,YAAY,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;IAC/C,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,MAAM,CAAC;IAChB,CAAC;IAED,MAAM,QAAQ,GAAG,OAAO,CAAC,OAAO,CAAC,WAAW,CAAC,CAAC;IAC9C,MAAM,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;IAC1C,IAAI,QAAQ,KAAK,CAAC,CAAC,IAAI,MAAM,IAAI,QAAQ;QAAE,OAAO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package/lib/dist/installer/targets/types.d.ts

@@ -63,6 +63,13 @@ export interface InstallOptions {
      * target has no permissions concept this option is a no-op.
      */
     autoAllow: boolean;
+    /**
+     * Front-load prompt hook (Claude `UserPromptSubmit`) that injects
+     * codegraph_explore context for structural prompts. `true` installs it,
+     * `false` removes any prior install (so opt-out round-trips), `undefined`
+     * leaves it untouched. Targets without a prompt-hook concept ignore it.
+     */
+    promptHook?: boolean;
 }
 export interface AgentTarget {
     /** Stable id; matches the `TargetId` union. */

package/lib/dist/installer/targets/types.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"engine.d.ts","sourceRoot":"","sources":["../../src/mcp/engine.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAKH,OAAO,EAAE,WAAW,EAAE,MAAM,SAAS,CAAC;AAWtC,MAAM,WAAW,gBAAgB;IAC/B;;;;OAIG;IACH,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAED;;;;;GAKG;AACH,qBAAa,SAAS;IACpB,OAAO,CAAC,EAAE,CAA0B;IACpC,OAAO,CAAC,WAAW,CAAc;IAIjC,OAAO,CAAC,WAAW,CAAuB;IAE1C,OAAO,CAAC,WAAW,CAA8B;IACjD,OAAO,CAAC,cAAc,CAAS;IAC/B,OAAO,CAAC,IAAI,CAA6B;IACzC,OAAO,CAAC,MAAM,CAAS;gBAEX,IAAI,GAAE,gBAAqB;IAKvC;;;;;OAKG;IACH,kBAAkB,CAAC,WAAW,EAAE,MAAM,GAAG,IAAI;IAK7C,0EAA0E;IAC1E,cAAc,IAAI,MAAM,GAAG,IAAI;IAI/B,yEAAyE;IACzE,cAAc,IAAI,WAAW;IAI7B,uDAAuD;IACvD,mBAAmB,IAAI,OAAO;IAI9B;;;;;;;;OAQG;IACG,iBAAiB,CAAC,UAAU,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAmB1D;;;;OAIG;IACH,mBAAmB,CAAC,UAAU,EAAE,MAAM,GAAG,IAAI;IAsB7C;;;OAGG;IACH,IAAI,IAAI,IAAI;YAUE,YAAY;IAsB1B;;;;;;OAMG;IACH,OAAO,CAAC,aAAa;IA+CrB;;;;;;;;;OASG;IACH,OAAO,CAAC,WAAW;CAiBpB;AAED;;;;;;;;;;;;GAYG;AACH,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,SAAS,GAAG,MAAM,GAAG,SAAS,CAM5E"}
+{"version":3,"file":"engine.d.ts","sourceRoot":"","sources":["../../src/mcp/engine.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAKH,OAAO,EAAE,WAAW,EAAE,MAAM,SAAS,CAAC;AAWtC,MAAM,WAAW,gBAAgB;IAC/B;;;;OAIG;IACH,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAED;;;;;GAKG;AACH,qBAAa,SAAS;IACpB,OAAO,CAAC,EAAE,CAA0B;IACpC,OAAO,CAAC,WAAW,CAAc;IAIjC,OAAO,CAAC,WAAW,CAAuB;IAE1C,OAAO,CAAC,WAAW,CAA8B;IACjD,OAAO,CAAC,cAAc,CAAS;IAC/B,OAAO,CAAC,IAAI,CAA6B;IACzC,OAAO,CAAC,MAAM,CAAS;gBAEX,IAAI,GAAE,gBAAqB;IAKvC;;;;;OAKG;IACH,kBAAkB,CAAC,WAAW,EAAE,MAAM,GAAG,IAAI;IAK7C,0EAA0E;IAC1E,cAAc,IAAI,MAAM,GAAG,IAAI;IAI/B,yEAAyE;IACzE,cAAc,IAAI,WAAW;IAI7B,uDAAuD;IACvD,mBAAmB,IAAI,OAAO;IAI9B;;;;;;;;OAQG;IACG,iBAAiB,CAAC,UAAU,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAmB1D;;;;OAIG;IACH,mBAAmB,CAAC,UAAU,EAAE,MAAM,GAAG,IAAI;IAsB7C;;;OAGG;IACH,IAAI,IAAI,IAAI;YAUE,YAAY;IAsB1B;;;;;;OAMG;IACH,OAAO,CAAC,aAAa;IAuDrB;;;;;;;;;OASG;IACH,OAAO,CAAC,WAAW;CAiBpB;AAED;;;;;;;;;;;;GAYG;AACH,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,SAAS,GAAG,MAAM,GAAG,SAAS,CAM5E"}

package/lib/dist/mcp/engine.js

@@ -205,6 +205,14 @@ class MCPEngine {
             onSyncError: (err) => {
                 process.stderr.write(`[CodeGraph MCP] Auto-sync error: ${err.message}\n`);
             },
+            onDegraded: (reason) => {
+                // Live watching gave up permanently (watch-resource exhaustion or a
+                // write lock held past the retry budget). Say so loudly and ONCE — the
+                // graph will no longer auto-update, so a long-running MCP session must
+                // not keep assuming it's fresh. The reason already names the remedy
+                // (`codegraph sync` / git sync hooks).
+                process.stderr.write(`[CodeGraph MCP] File watcher degraded — ${reason}\n`);
+            },
         });
         this.watcherStarted = true;
         if (started) {

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

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

@@ -7,24 +7,28 @@
  * before it sees individual tool descriptions.
  *
  * Goals when editing this:
- *   - Tool selection by intent (which tool for which question)
- *   - Common chains (refactor planning = X then Y)
- *   - Anti-patterns (don't grep when codegraph_search is faster)
+ *   - Lead the agent to codegraph_explore for any structural/flow question
+ *   - Reinforce "explore instead of Read/Grep" for indexed code
+ *   - Anti-patterns (don't re-verify with grep; don't hand-reconstruct flows)
  *
  * Keep it tight. The agent reads this every session — long instructions
- * burn tokens. Reference only tools that exist on `main`; gate any
- * conditional tools behind feature checks if/when they ship.
+ * burn tokens. The DEFAULT MCP surface is `codegraph_explore` ALONE (see
+ * DEFAULT_MCP_TOOLS in tools.ts) — reference only that tool here. The other
+ * tools (node/search/callers/…) stay defined and are re-enablable via
+ * CODEGRAPH_MCP_TOOLS, but they are NOT listed to agents, so don't name them.
  */
-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 in\nthe workspace \u2014 pre-computed structure you would otherwise re-derive by\nreading files (cached intelligence: thousands of parse/trace decisions you\ndon't pay to re-reason each run). Reads are sub-millisecond; the index lags\nwrites by ~1s through the file watcher. Reach for it BEFORE *and* while\nwriting or editing code \u2014 not just for questions: one call returns the\nverbatim source PLUS who calls it and what it affects, so you edit with the\nblast radius in view. More accurate context, in far fewer tokens and\nround-trips than reading files yourself.\n\n## Use codegraph instead of reading files \u2014 for questions AND edits\n\nWhether you're answering \"how does X work\" or implementing a change (fixing\na bug, adding a feature), reach for codegraph before you Read. For\nunderstanding, answer DIRECTLY \u2014 usually with ONE `codegraph_explore` call.\n`codegraph_explore` takes either a natural-language question or a bag of\nsymbol/file names and returns the verbatim source of the relevant symbols\ngrouped by file, so it is Read-equivalent and most often the ONLY\ncodegraph call you need. Codegraph IS the pre-built search index \u2014 so\ndelegating the lookup to a separate file-reading sub-task/agent, or\nrunning your own grep + read loop, repeats work codegraph already did and\ncosts more for the same answer. Reach for raw Read/Grep only to confirm a\nspecific detail codegraph didn't cover. A direct codegraph answer is\ntypically one to a few calls; a grep/read exploration is dozens.\n\n## Tool selection by intent\n\n- **Almost any question \u2014 \"how does X work\", architecture, a bug, \"what/where is X\", or surveying an area** \u2192 `codegraph_explore` (PRIMARY \u2014 call FIRST; ONE capped call returns the verbatim source of the relevant symbols grouped by file; most often the ONLY call you need)\n- **\"How does X reach/become Y? / the flow / the path from X to Y\"** \u2192 `codegraph_explore`, naming the symbols that span the flow (e.g. `mutateElement renderScene`) \u2014 it surfaces the call path among them, including dynamic-dispatch hops (callbacks, React re-render, JSX children) grep can't follow\n- **\"What is the symbol named X?\" (just its location)** \u2192 `codegraph_search`\n- **\"What calls this?\" / \"What would changing this break?\"** \u2192 `codegraph_callers` \u2014 EVERY call site with file:line, including where a function is **registered as a callback** (passed as an argument, assigned to a function pointer/field, listed in a handler table) \u2014 labeled \"via callback registration\" \u2014 so a function with no direct calls is NOT dead if it's wired up somewhere. When several UNRELATED symbols share a name (one `UserService` per monorepo app), it reports **one section per definition** (never a merged list) \u2014 pass `file` to focus the definition you mean. The wider blast radius arrives automatically on `codegraph_explore` (its \"Blast radius\" section) and `codegraph_node` (the dependents note)\n- **\"What does this call?\"** \u2192 `codegraph_node` with that symbol and `includeCode: true` \u2014 the body IS the callee list, and the caller/callee trail comes with it\n- **Reading a source FILE (any time you'd use the `Read` tool)** \u2192 `codegraph_node` with a `file` path and no `symbol`. It returns the file's **current source with line numbers \u2014 the same `<n>\\t<line>` shape `Read` gives you, safe to `Edit` from** \u2014 narrowable with `offset`/`limit` exactly like `Read`, PLUS a one-line note of which files depend on it. Same bytes as `Read`, faster (served from the index), with the blast radius attached. Use it **instead of `Read`** for indexed source files; fall back to `Read` only for what codegraph doesn't index (configs, docs). Pass `symbolsOnly: true` for just the file's structure.\n- **About to read or edit a symbol you can name** \u2192 `codegraph_node` with that `symbol` (SECONDARY \u2014 the after-explore depth tool): the verbatim source (`includeCode: true`) PLUS its caller/callee trail, so before changing it you see what calls it and what your edit would break. For an OVERLOADED name it returns EVERY matching definition's body in one call, so you never Read a file to find the right overload\n\n## Common chains\n\n- **Flow / \"how does X reach Y\"**: ONE `codegraph_explore` with the symbol names spanning the flow \u2014 it surfaces the call path among them (riding dynamic-dispatch hops) AND returns their source. No need to reconstruct the path with `codegraph_search` + `codegraph_callers`.\n- **Onboarding / understanding any area**: ONE `codegraph_explore` is usually the whole answer. Only follow up \u2014 `codegraph_node` for a specific symbol \u2014 if something is still unclear.\n- **Refactor planning**: `codegraph_callers` for the complete call-site list to update; the wider blast radius is already attached to `codegraph_explore` / `codegraph_node` output.\n- **Debugging a regression**: `codegraph_callers` of the suspected symbol; `codegraph_node` on anything unexpected that appears.\n\n## Anti-patterns\n\n- **Trust codegraph's results \u2014 don't re-verify them with grep.** They come from a full AST parse; re-checking with grep is slower, less accurate, and wastes context.\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`** to understand an area \u2014 ONE `codegraph_explore` returns the relevant symbols' source together in a single 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 reach for the `Read` tool on an indexed source file** \u2014 `codegraph_node` with a `file` reads it for you (same `<n>\\t<line>` source, `offset`/`limit` like Read, faster, with its blast radius), and with a `symbol` it returns the source plus the caller/callee trail. Reach for raw `Read` only for what codegraph doesn't index (configs, docs) or when the staleness banner flags a file as pending re-index.\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.\n\n## Limitations\n\n- If a tool reports a project isn't indexed (no `.codegraph/`), stop calling codegraph tools for that project for the rest of the session and use your built-in tools there instead. Indexing is the user's decision \u2014 mention they can run `codegraph init` if it comes up, but don't run it yourself.\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 in\nthe workspace \u2014 pre-computed structure you would otherwise re-derive by\nreading files (cached intelligence: thousands of parse/trace decisions you\ndon't pay to re-reason each run). Reads are sub-millisecond; the index lags\nwrites by ~1s through the file watcher. Reach for it BEFORE *and* while\nwriting or editing code \u2014 not just for questions: one call returns the\nverbatim source PLUS who calls it and what it affects, so you edit with the\nblast radius in view. More accurate context, in far fewer tokens and\nround-trips than reading files yourself.\n\n## One tool: codegraph_explore \u2014 use it instead of reading files\n\nThere is a single tool, `codegraph_explore`, and it is Read-equivalent. It\ntakes either a natural-language question or a bag of symbol/file names and\nreturns the **verbatim, line-numbered source** of the relevant symbols\ngrouped by file \u2014 the same `<n>\\t<line>` shape `Read` gives you, safe to\n`Edit` from \u2014 PLUS the call path among them (including dynamic-dispatch hops\nlike callbacks, React re-render, and JSX children that grep can't follow) and\na blast-radius summary of what depends on them.\n\nWhether you're answering \"how does X work\" or implementing a change (fixing a\nbug, adding a feature), call `codegraph_explore` before you Read. ONE call\nusually answers the whole question. Codegraph IS the pre-built search index \u2014\nso running your own grep + read loop, or delegating the lookup to a separate\nfile-reading sub-task/agent, repeats work codegraph already did and costs more\nfor the same answer. A direct codegraph answer is typically one to a few\ncalls; a grep/read exploration is dozens.\n\n## How to query\n\n- **Almost any question \u2014 \"how does X work\", architecture, a bug, \"what/where is X\", or surveying an area** \u2192 `codegraph_explore` with a natural-language question or the relevant names. ONE capped call returns the verbatim source grouped by file; most often the ONLY call you need.\n- **\"How does X reach/become Y? / the flow / the path from X to Y\"** \u2192 `codegraph_explore`, naming the symbols that span the flow (e.g. `mutateElement renderScene`) \u2014 it surfaces the call path among them, riding dynamic-dispatch hops, and returns their source.\n- **Reading or editing a file/symbol you can name** \u2192 put its name or file path in the `codegraph_explore` query \u2014 it returns that current line-numbered source (safe to `Edit` from) with the call path and blast radius attached, so you don't Read it separately. For an overloaded name it returns every matching definition's body in one call.\n- **Need more?** Call `codegraph_explore` again with more specific names \u2014 treat the source it returns as already Read.\n\n## Anti-patterns\n\n- **Trust codegraph's results \u2014 don't re-verify them with grep.** They come from a full AST parse; re-checking with grep is slower, less accurate, and wastes context.\n- **Don't grep or Read first** to find or understand indexed code \u2014 ONE `codegraph_explore` returns the relevant symbols' source together in a single round-trip. Reach for raw `Read`/`Grep` only to confirm a specific detail codegraph didn't cover, or for what codegraph doesn't index (configs, docs).\n- **Don't reconstruct a flow by hand** \u2014 name the endpoints in one `codegraph_explore` and it surfaces the path between them, dynamic-dispatch hops included.\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. A different, rarer banner \u2014 \"\u26A0\uFE0F CodeGraph auto-sync is DISABLED\u2026\" \u2014 means live watching stopped entirely (the whole index is frozen, not just a few files); until it's resolved, Read files directly to confirm anything that may have changed.\n\n## Limitations\n\n- If a tool reports a project isn't indexed (no `.codegraph/`), stop calling codegraph tools for that project for the rest of the session and use your built-in tools there instead. Indexing is the user's decision \u2014 mention they can run `codegraph init` if it comes up, but don't run it yourself.\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";
 /**
- * Instructions variant sent when the workspace has NO codegraph index.
+ * Instructions variant sent when the server's own root has NO codegraph index.
  *
- * Sending the full playbook ("lean on codegraph for everything") into a
- * session where every call would fail wastes the agent's calls and — worse —
- * the failures teach it codegraph is broken. The unindexed variant is a
- * short, unambiguous "inactive this session" note; `tools/list` is gated to
- * empty in the same state, so the agent has nothing to mis-call. Indexing is
- * deliberately left to the user: the agent is told NOT to run init itself.
+ * The tools are still exposed (gating tool availability on whether `./` has an
+ * index is the bug behind #964: it breaks monorepos where only sub-projects are
+ * indexed, and a server that started before `codegraph init` never surfaces the
+ * tools afterward). Instead of an "inactive" note, this variant tells the agent
+ * codegraph works **per project**: there's no default project to query, so pass
+ * a `projectPath` to any project that HAS a `.codegraph/`. The full single-
+ * project playbook ({@link SERVER_INSTRUCTIONS}) is sent instead when the root
+ * IS indexed, so the common case stays tight.
  */
-export declare const SERVER_INSTRUCTIONS_UNINDEXED = "# Codegraph \u2014 inactive (workspace not indexed)\n\nThis workspace has no codegraph index (no `.codegraph/` directory), so no\ncodegraph tools are available this session. Work with your built-in tools as\nusual.\n\nIndexing is the user's decision \u2014 do not run it yourself. If the user asks\nabout codegraph, they can enable it by running `codegraph init` in the\nproject root and starting a new session.\n";
+export declare const SERVER_INSTRUCTIONS_NO_ROOT_INDEX = "# Codegraph \u2014 available (per-project; pass projectPath)\n\nCodegraph is a SQLite knowledge graph of a codebase's symbols, edges, and\nfiles: one `codegraph_explore` call returns the verbatim, line-numbered source\nof the relevant symbols PLUS the call paths between them and a blast-radius\nsummary \u2014 replacing a grep + Read loop with one round-trip.\n\nThis server started somewhere with no `.codegraph/` of its own, so there is no\ndefault project \u2014 but the tools are available and work **per project**:\n\n- To query a project that HAS a `.codegraph/` index (e.g. a service inside a\n  monorepo, or a second repo), pass its path as `projectPath` to\n  `codegraph_explore` (and any other codegraph tool). Codegraph resolves the\n  nearest `.codegraph/` at or above that path and answers from it \u2014 for as many\n  projects as you like in one session.\n- For a project with no `.codegraph/`, use your built-in tools (Read/Grep/Glob)\n  for that project. Indexing is the user's decision \u2014 don't run it yourself, but\n  if it comes up they can run `codegraph init` in a project to enable codegraph\n  there (a new index is picked up live, no restart).\n";
 //# sourceMappingURL=server-instructions.d.ts.map

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

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