@blamechris/repo-memory 0.11.0 → 0.13.0

package/dist/indexer/summarize.js

@@ -1,24 +1,11 @@
 import { loadConfig } from '../config.js';
 import { CacheStore } from '../cache/store.js';
+import { GENERATION_META_KEY, currentSummarizerGeneration, isStoredGenerationNewer, } from '../cache/generation.js';
 import { summarizeFile } from './summarizer.js';
 import { summarizeFileAst } from './ast-summarizer.js';
-/**
- * Bump when summary output changes in a way that should invalidate previously
- * cached summaries (combined with the mode into the generation tag).
- *
- * Generation 2: the AST summarizer gained Python/Go/Rust support, so summaries
- * for those languages cached under ast mode (which were regex-produced
- * fallbacks at generation 1) must lazily regenerate.
- *
- * Generation 3: the AST summarizer gained Kotlin/Java support, so summaries
- * for those languages cached under ast mode (regex-produced generic
- * classifications at earlier generations) must lazily regenerate.
- */
-const SUMMARIZER_GENERATION = 3;
-const META_KEY = 'summarizer_generation';
 const generationChecked = new Map();
 export function getSummarizerMode(projectRoot) {
-    return loadConfig(projectRoot).summarizer ?? 'regex';
+    return loadConfig(projectRoot).summarizer ?? 'ast';
 }
 /** Generate a summary using the summarizer configured for this project. */
 export async function summarizeForProject(projectRoot, filePath, contents) {
@@ -31,28 +18,56 @@ export async function summarizeForProject(projectRoot, filePath, contents) {
  * Ensure cached summaries were produced by the currently configured
  * summarizer. When the mode (or generation) changes, all stored summaries are
  * dropped — hashes stay, so change detection is unaffected and summaries
- * regenerate lazily — and the new generation tag is recorded.
+ * regenerate lazily — and the new generation tag is recorded, atomically with
+ * the clear.
+ *
+ * Generations are monotonic: when the stored tag belongs to a *newer*
+ * generation than this process (e.g. an npx post-merge hook at a newer
+ * package version retagged the cache while this long-running server kept an
+ * older build in memory), this process must not clear, must not regress the
+ * tag, and must not persist its own summaries. It keeps working read-through:
+ * summaries it computes are served from memory, and CacheStore strips them on
+ * write (see setEntry/setEntries), so the cache never mixes generations and
+ * old/new version alternation cannot cause clear-storms. Mode flips (regex vs
+ * ast) at the same numeric generation are last-writer-wins by design — see
+ * src/cache/generation.ts.
  *
  * Must run before any cache lookup that can return a stored summary.
  */
 export function ensureSummaryGeneration(projectRoot) {
-    const tag = `${getSummarizerMode(projectRoot)}:${SUMMARIZER_GENERATION}`;
+    const tag = `${getSummarizerMode(projectRoot)}:${currentSummarizerGeneration()}`;
     if (generationChecked.get(projectRoot) === tag)
         return;
     const store = new CacheStore(projectRoot);
-    const stored = store.getMeta(META_KEY);
-    if (stored !== tag) {
+    // Read-decide-write under the write lock, so another process cannot bump
+    // the generation between our read of the tag and our clear (Guardian I3).
+    const reconciled = store.withWriteLock(() => {
+        const stored = store.getMeta(GENERATION_META_KEY);
+        if (stored === tag)
+            return true;
+        if (isStoredGenerationNewer(stored)) {
+            // Never downgrade — a newer package version owns this cache.
+            return false;
+        }
         // Regex output is unchanged since generation 1, so summaries produced by
         // any earlier regex generation — including pre-marker databases, which
         // carried no tag — are still valid under regex generation 3 and only need
         // re-tagging.
         const stillValid = tag === 'regex:3' && (stored === null || /^regex:[12]$/.test(stored));
-        if (!stillValid) {
-            store.clearAllSummaries();
+        if (stillValid) {
+            store.setMeta(GENERATION_META_KEY, tag);
         }
-        store.setMeta(META_KEY, tag);
-    }
-    generationChecked.set(projectRoot, tag);
+        else {
+            store.clearAllSummariesAndSetMeta(GENERATION_META_KEY, tag);
+        }
+        return true;
+    });
+    // Memoize the happy path only. A process running behind the stored
+    // generation re-checks on every call (one cheap row read) so it recovers
+    // immediately if it is ever upgraded in place; its summary writes are
+    // independently guarded inside CacheStore either way.
+    if (reconciled)
+        generationChecked.set(projectRoot, tag);
 }
 /** Test hook: forget which projects already had their generation verified. */
 export function clearSummaryGenerationCache() {

package/dist/indexer/summarize.js.map

@@ -1 +1 @@
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+{"version":3,"file":"summarize.js","sourceRoot":"","sources":["../../src/indexer/summarize.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,cAAc,CAAC;AAC1C,OAAO,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AAC/C,OAAO,EACL,mBAAmB,EACnB,2BAA2B,EAC3B,uBAAuB,GACxB,MAAM,wBAAwB,CAAC;AAChC,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,qBAAqB,CAAC;AAavD,MAAM,iBAAiB,GAAG,IAAI,GAAG,EAAkB,CAAC;AAEpD,MAAM,UAAU,iBAAiB,CAAC,WAAmB;IACnD,OAAO,UAAU,CAAC,WAAW,CAAC,CAAC,UAAU,IAAI,KAAK,CAAC;AACrD,CAAC;AAED,2EAA2E;AAC3E,MAAM,CAAC,KAAK,UAAU,mBAAmB,CACvC,WAAmB,EACnB,QAAgB,EAChB,QAAgB;IAEhB,IAAI,iBAAiB,CAAC,WAAW,CAAC,KAAK,KAAK,EAAE,CAAC;QAC7C,OAAO,gBAAgB,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAC;IAC9C,CAAC;IACD,OAAO,aAAa,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAC;AAC3C,CAAC;AAED;;;;;;;;;;;;;;;;;;;GAmBG;AACH,MAAM,UAAU,uBAAuB,CAAC,WAAmB;IACzD,MAAM,GAAG,GAAG,GAAG,iBAAiB,CAAC,WAAW,CAAC,IAAI,2BAA2B,EAAE,EAAE,CAAC;IACjF,IAAI,iBAAiB,CAAC,GAAG,CAAC,WAAW,CAAC,KAAK,GAAG;QAAE,OAAO;IAEvD,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,WAAW,CAAC,CAAC;IAC1C,yEAAyE;IACzE,0EAA0E;IAC1E,MAAM,UAAU,GAAG,KAAK,CAAC,aAAa,CAAC,GAAG,EAAE;QAC1C,MAAM,MAAM,GAAG,KAAK,CAAC,OAAO,CAAC,mBAAmB,CAAC,CAAC;QAClD,IAAI,MAAM,KAAK,GAAG;YAAE,OAAO,IAAI,CAAC;QAChC,IAAI,uBAAuB,CAAC,MAAM,CAAC,EAAE,CAAC;YACpC,6DAA6D;YAC7D,OAAO,KAAK,CAAC;QACf,CAAC;QACD,yEAAyE;QACzE,uEAAuE;QACvE,0EAA0E;QAC1E,cAAc;QACd,MAAM,UAAU,GAAG,GAAG,KAAK,SAAS,IAAI,CAAC,MAAM,KAAK,IAAI,IAAI,cAAc,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC;QACzF,IAAI,UAAU,EAAE,CAAC;YACf,KAAK,CAAC,OAAO,CAAC,mBAAmB,EAAE,GAAG,CAAC,CAAC;QAC1C,CAAC;aAAM,CAAC;YACN,KAAK,CAAC,2BAA2B,CAAC,mBAAmB,EAAE,GAAG,CAAC,CAAC;QAC9D,CAAC;QACD,OAAO,IAAI,CAAC;IACd,CAAC,CAAC,CAAC;IAEH,mEAAmE;IACnE,yEAAyE;IACzE,sEAAsE;IACtE,sDAAsD;IACtD,IAAI,UAAU;QAAE,iBAAiB,CAAC,GAAG,CAAC,WAAW,EAAE,GAAG,CAAC,CAAC;AAC1D,CAAC;AAED,8EAA8E;AAC9E,MAAM,UAAU,2BAA2B;IACzC,iBAAiB,CAAC,KAAK,EAAE,CAAC;AAC5B,CAAC"}

package/dist/persistence/db.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"db.d.ts","sourceRoot":"","sources":["../../src/persistence/db.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,gBAAgB,CAAC;AA2MtC,wFAAwF;AACxF,wBAAgB,eAAe,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,CAE3D;AAED,wBAAgB,WAAW,CAAC,WAAW,EAAE,MAAM,GAAG,QAAQ,CAAC,QAAQ,CA6BlE;AAED,wBAAgB,aAAa,IAAI,IAAI,CAMpC"}

package/dist/persistence/db.js

@@ -102,20 +102,40 @@ const MIGRATIONS = [
         },
     },
 ];
-function runMigrations(db) {
-    db.exec(`
-    CREATE TABLE IF NOT EXISTS schema_version (
-      version INTEGER PRIMARY KEY,
-      applied_at INTEGER NOT NULL
-    );
-  `);
+function latestMigrationVersion() {
+    return Math.max(...MIGRATIONS.map((m) => m.version));
+}
+function appliedSchemaVersion(db) {
     const applied = db
         .prepare('SELECT version FROM schema_version ORDER BY version DESC LIMIT 1')
         .get();
-    const currentVersion = applied?.version ?? 0;
-    const sortedMigrations = [...MIGRATIONS].sort((a, b) => a.version - b.version);
-    const insertVersion = db.prepare('INSERT INTO schema_version (version, applied_at) VALUES (?, ?)');
+    return applied?.version ?? 0;
+}
+/**
+ * Concurrent-safe migrations (Guardian I9). Two processes opening a fresh
+ * database at the same time (MCP server start + post-merge hook prewarm) must
+ * both succeed:
+ *
+ * - The whole sequence runs under BEGIN IMMEDIATE, so competing processes
+ *   serialize: the loser waits on the write lock (up to busy_timeout) instead
+ *   of interleaving.
+ * - `schema_version` is read *inside* the transaction, so the loser sees the
+ *   winner's rows once it gets the lock and applies nothing.
+ * - If the transaction still fails (busy_timeout exceeded, or a constraint
+ *   from a writer not using this protocol), the failure is tolerated when
+ *   another process has already completed the migrations.
+ */
+function runMigrations(db) {
     const applyMigrations = db.transaction(() => {
+        db.exec(`
+      CREATE TABLE IF NOT EXISTS schema_version (
+        version INTEGER PRIMARY KEY,
+        applied_at INTEGER NOT NULL
+      );
+    `);
+        const currentVersion = appliedSchemaVersion(db);
+        const sortedMigrations = [...MIGRATIONS].sort((a, b) => a.version - b.version);
+        const insertVersion = db.prepare('INSERT INTO schema_version (version, applied_at) VALUES (?, ?)');
         for (const migration of sortedMigrations) {
             if (migration.version > currentVersion) {
                 migration.up(db);
@@ -123,7 +143,51 @@ function runMigrations(db) {
             }
         }
     });
-    applyMigrations();
+    try {
+        applyMigrations.immediate();
+    }
+    catch (err) {
+        if (migrationsAlreadyApplied(db)) {
+            return; // lost the race; another process migrated the database
+        }
+        throw err;
+    }
+}
+function migrationsAlreadyApplied(db) {
+    try {
+        return appliedSchemaVersion(db) >= latestMigrationVersion();
+    }
+    catch {
+        return false; // schema_version table itself is missing or unreadable
+    }
+}
+/**
+ * Switching a fresh database into WAL takes a brief exclusive lock, and SQLite
+ * returns SQLITE_BUSY from a journal-mode change *without invoking the busy
+ * handler* when another connection holds a conflicting lock — so the
+ * connection's busy_timeout does not cover this one statement. Two processes
+ * opening a brand-new database together (MCP server start + post-merge hook
+ * prewarm) hit exactly that, so retry briefly. Once the database is in WAL
+ * the pragma is a no-op and never contends again.
+ */
+function enableWalMode(db) {
+    const deadline = Date.now() + 5000;
+    for (;;) {
+        try {
+            db.pragma('journal_mode = WAL');
+            return;
+        }
+        catch (err) {
+            if (err.code !== 'SQLITE_BUSY' || Date.now() >= deadline) {
+                throw err;
+            }
+            sleepSync(10);
+        }
+    }
+}
+/** Synchronous sleep without blocking-spin (better-sqlite3 is a sync API). */
+function sleepSync(ms) {
+    Atomics.wait(new Int32Array(new SharedArrayBuffer(4)), 0, 0, ms);
 }
 /** Absolute path of the cache database for a project (whether or not it exists yet). */
 export function getDatabasePath(projectRoot) {
@@ -143,8 +207,9 @@ export function getDatabase(projectRoot) {
     if (!existsSync(dbDir)) {
         mkdirSync(dbDir, { recursive: true });
     }
-    const db = new Database(dbPath);
-    db.pragma('journal_mode = WAL');
+    const db = new Database(dbPath, { timeout: 5000 });
+    enableWalMode(db);
+    db.pragma('busy_timeout = 5000');
     db.pragma('foreign_keys = ON');
     runMigrations(db);
     instance = db;

package/dist/persistence/db.js.map

@@ -1 +1 @@
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package/dist/server.js

@@ -30,20 +30,23 @@ function registerTools(server, config) {
     // === NAVIGATION GROUP (always on) ===
     server.registerTool('get_project_map', {
         title: 'Get Project Map',
-        description: 'Returns a structural overview of the project including directory tree, entry points, and key modules.',
+        description: 'Returns a structural overview of the project including directory tree, entry points, and key modules. Depth defaults to 2; pass a larger depth only when you need deeper structure.',
         inputSchema: {
-            project_root: z.string().describe('Absolute path to the project root'),
-            depth: z.number().optional().describe('Max directory depth to include'),
+            project_root: z
+                .string()
+                .optional()
+                .describe('Absolute path to the project root (default: current working directory)'),
+            depth: z.number().optional().describe('Max directory depth to include (default: 2)'),
         },
     }, async ({ project_root, depth }) => {
-        const projectMap = await getProjectMap(project_root, depth);
+        const projectMap = await getProjectMap(project_root ?? process.cwd(), depth);
         return {
             content: [{ type: 'text', text: JSON.stringify(projectMap) }],
         };
     });
     server.registerTool('get_related_files', {
         title: 'Get Related Files',
-        description: 'Returns files related to the given file, ranked by dependency proximity and relevance. Useful for finding what else to look at when exploring a file.',
+        description: 'Returns files related to the given file, ranked by dependency proximity and relevance. One call replaces grepping for imports and grepping for usages separately.',
         inputSchema: {
             path: z.string().describe('File path relative to project root'),
             limit: z.number().optional().describe('Max results (default: 10)'),
@@ -58,19 +61,23 @@ function registerTools(server, config) {
     });
     server.registerTool('get_dependency_graph', {
         title: 'Get Dependency Graph',
-        description: 'Returns dependency graph information. If a path is given, returns its dependencies/dependents. If no path, returns a summary of the most connected files.',
+        description: 'Returns dependency graph information as adjacency maps. If a path is given, returns its dependencies/dependents. Calling without a path returns a large whole-repo summary of the most connected files — prefer passing a path.',
         inputSchema: {
-            path: z.string().optional().describe('File path to query, or omit for full graph summary'),
+            path: z.string().optional().describe('File path to query; omit only when you want a whole-repo summary'),
             direction: z
                 .enum(['dependencies', 'dependents', 'both'])
                 .optional()
                 .describe('Query direction (default: both)'),
             depth: z.number().optional().describe('Max traversal depth'),
             symbol: z.string().optional().describe('Filter edges by import specifier (e.g., "UserService")'),
+            limit: z
+                .number()
+                .optional()
+                .describe('No-path summary mode only: max files included (default: 50)'),
         },
-    }, async ({ path, direction, depth, symbol }) => {
+    }, async ({ path, direction, depth, symbol, limit }) => {
         const projectRoot = process.cwd();
-        const result = await getDependencyGraphTool(projectRoot, path, direction, depth, symbol);
+        const result = await getDependencyGraphTool(projectRoot, path, direction, depth, symbol, limit);
         return {
             content: [{ type: 'text', text: JSON.stringify(result) }],
         };
@@ -150,7 +157,7 @@ function registerTools(server, config) {
         });
         server.registerTool('search_by_purpose', {
             title: 'Search By Purpose',
-            description: 'Search cached file summaries by keyword. Matches against file purpose, exports, and declarations. Requires files to have been previously summarized. Optionally scope to a directory with pathPrefix.',
+            description: 'Find files by what they do when you don\'t know filenames — prefer this over grep for concept searches ("where is auth handled"). Matches against file purpose, exports, and declarations. Check totalCached > 0 in the response; if 0, warm the cache with `repo-memory index` first. Optionally scope to a directory with pathPrefix.',
             inputSchema: {
                 query: z.string().describe('Search keywords (e.g., "database", "auth middleware", "validation")'),
                 limit: z.number().optional().describe('Max results (default: 20)'),
@@ -158,7 +165,7 @@ function registerTools(server, config) {
             },
         }, async ({ query, limit, pathPrefix }) => {
             const projectRoot = process.cwd();
-            const result = searchByPurpose(projectRoot, query, limit, pathPrefix);
+            const result = await searchByPurpose(projectRoot, query, limit, pathPrefix);
             return {
                 content: [{ type: 'text', text: JSON.stringify(result) }],
             };

package/dist/server.js.map

@@ -1 +1 @@
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package/dist/tools/batch-file-summaries.d.ts

@@ -1,7 +1,6 @@
 import { type FileSummaryResult } from './get-file-summary.js';
 export interface BatchFileSummariesResult {
     results: FileSummaryResult[];
-    totalFiles: number;
     cacheHits: number;
     cacheMisses: number;
     errors: Array<{

package/dist/tools/batch-file-summaries.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"batch-file-summaries.d.ts","sourceRoot":"","sources":["../../src/tools/batch-file-summaries.ts"],"names":[],"mappings":"AAAA,OAAO,EAAkB,KAAK,iBAAiB,EAAE,MAAM,uBAAuB,CAAC;AAG/E,MAAM,WAAW,wBAAwB;IACvC,OAAO,EAAE,iBAAiB,EAAE,CAAC;IAC7B,UAAU,EAAE,MAAM,CAAC;IACnB,SAAS,EAAE,MAAM,CAAC;IAClB,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;CAChD;AAED,wBAAsB,kBAAkB,CACtC,WAAW,EAAE,MAAM,EACnB,KAAK,EAAE,MAAM,EAAE,GACd,OAAO,CAAC,wBAAwB,CAAC,CAoBnC"}
+{"version":3,"file":"batch-file-summaries.d.ts","sourceRoot":"","sources":["../../src/tools/batch-file-summaries.ts"],"names":[],"mappings":"AAAA,OAAO,EAAkB,KAAK,iBAAiB,EAAE,MAAM,uBAAuB,CAAC;AAG/E,MAAM,WAAW,wBAAwB;IACvC,OAAO,EAAE,iBAAiB,EAAE,CAAC;IAC7B,SAAS,EAAE,MAAM,CAAC;IAClB,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;CAChD;AAED,wBAAsB,kBAAkB,CACtC,WAAW,EAAE,MAAM,EACnB,KAAK,EAAE,MAAM,EAAE,GACd,OAAO,CAAC,wBAAwB,CAAC,CAoBnC"}

package/dist/tools/batch-file-summaries.js

@@ -20,6 +20,6 @@ export async function batchFileSummaries(projectRoot, paths) {
             errors.push({ path: rawPath, error: message });
         }
     }
-    return { results, totalFiles: paths.length, cacheHits, cacheMisses, errors };
+    return { results, cacheHits, cacheMisses, errors };
 }
 //# sourceMappingURL=batch-file-summaries.js.map

package/dist/tools/batch-file-summaries.js.map

@@ -1 +1 @@
-{"version":3,"file":"batch-file-summaries.js","sourceRoot":"","sources":["../../src/tools/batch-file-summaries.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAA0B,MAAM,uBAAuB,CAAC;AAC/E,OAAO,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AAUzD,MAAM,CAAC,KAAK,UAAU,kBAAkB,CACtC,WAAmB,EACnB,KAAe;IAEf,MAAM,OAAO,GAAwB,EAAE,CAAC;IACxC,MAAM,MAAM,GAA2C,EAAE,CAAC;IAC1D,IAAI,SAAS,GAAG,CAAC,CAAC;IAClB,IAAI,WAAW,GAAG,CAAC,CAAC;IAEpB,KAAK,MAAM,OAAO,IAAI,KAAK,EAAE,CAAC;QAC5B,IAAI,CAAC;YACH,MAAM,SAAS,GAAG,YAAY,CAAC,WAAW,EAAE,OAAO,CAAC,CAAC;YACrD,MAAM,MAAM,GAAG,MAAM,cAAc,CAAC,WAAW,EAAE,SAAS,CAAC,CAAC;YAC5D,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;YACrB,IAAI,MAAM,CAAC,SAAS;gBAAE,SAAS,EAAE,CAAC;;gBAC7B,WAAW,EAAE,CAAC;QACrB,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,MAAM,OAAO,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;YACvE,MAAM,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,CAAC,CAAC;QACjD,CAAC;IACH,CAAC;IAED,OAAO,EAAE,OAAO,EAAE,UAAU,EAAE,KAAK,CAAC,MAAM,EAAE,SAAS,EAAE,WAAW,EAAE,MAAM,EAAE,CAAC;AAC/E,CAAC"}
+{"version":3,"file":"batch-file-summaries.js","sourceRoot":"","sources":["../../src/tools/batch-file-summaries.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAA0B,MAAM,uBAAuB,CAAC;AAC/E,OAAO,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AASzD,MAAM,CAAC,KAAK,UAAU,kBAAkB,CACtC,WAAmB,EACnB,KAAe;IAEf,MAAM,OAAO,GAAwB,EAAE,CAAC;IACxC,MAAM,MAAM,GAA2C,EAAE,CAAC;IAC1D,IAAI,SAAS,GAAG,CAAC,CAAC;IAClB,IAAI,WAAW,GAAG,CAAC,CAAC;IAEpB,KAAK,MAAM,OAAO,IAAI,KAAK,EAAE,CAAC;QAC5B,IAAI,CAAC;YACH,MAAM,SAAS,GAAG,YAAY,CAAC,WAAW,EAAE,OAAO,CAAC,CAAC;YACrD,MAAM,MAAM,GAAG,MAAM,cAAc,CAAC,WAAW,EAAE,SAAS,CAAC,CAAC;YAC5D,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;YACrB,IAAI,MAAM,CAAC,SAAS;gBAAE,SAAS,EAAE,CAAC;;gBAC7B,WAAW,EAAE,CAAC;QACrB,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,MAAM,OAAO,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;YACvE,MAAM,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,CAAC,CAAC;QACjD,CAAC;IACH,CAAC;IAED,OAAO,EAAE,OAAO,EAAE,SAAS,EAAE,WAAW,EAAE,MAAM,EAAE,CAAC;AACrD,CAAC"}

package/dist/tools/force-reread.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"force-reread.d.ts","sourceRoot":"","sources":["../../src/tools/force-reread.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,aAAa,CAAC;AAG/C,wBAAsB,WAAW,CAC/B,WAAW,EAAE,MAAM,EACnB,YAAY,EAAE,MAAM,GACnB,OAAO,CAAC;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,WAAW,CAAC;IAAC,MAAM,EAAE,IAAI,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,CAAC,CAe7F"}
+{"version":3,"file":"force-reread.d.ts","sourceRoot":"","sources":["../../src/tools/force-reread.ts"],"names":[],"mappings":"AASA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,aAAa,CAAC;AAG/C,wBAAsB,WAAW,CAC/B,WAAW,EAAE,MAAM,EACnB,YAAY,EAAE,MAAM,GACnB,OAAO,CAAC;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,WAAW,CAAC;IAAC,MAAM,EAAE,IAAI,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,CAAC,CAoB7F"}

package/dist/tools/force-reread.js

@@ -2,7 +2,9 @@ import { readFile } from 'node:fs/promises';
 import { join } from 'node:path';
 import { hashContents } from '../cache/hash.js';
 import { CacheStore } from '../cache/store.js';
+import { isGraphIndexable } from '../indexer/source-extensions.js';
 import { summarizeForProject, ensureSummaryGeneration } from '../indexer/summarize.js';
+import { DependencyGraph } from '../graph/dependency-graph.js';
 import { TelemetryTracker } from '../telemetry/tracker.js';
 import { estimateTokens } from '../telemetry/tokens.js';
 import { validatePath } from '../utils/validate-path.js';
@@ -14,6 +16,11 @@ export async function forceReread(projectRoot, relativePath) {
     const hash = hashContents(contents);
     const summary = await summarizeForProject(projectRoot, relativePath, contents);
     const store = new CacheStore(projectRoot);
+    // Re-extract import edges from the fresh contents before recording the new
+    // hash (see get-file-summary.ts for the ordering rationale).
+    if (isGraphIndexable(relativePath)) {
+        new DependencyGraph(projectRoot).updateFile(relativePath, contents);
+    }
     store.setEntry(relativePath, hash, summary);
     const tracker = new TelemetryTracker(projectRoot);
     tracker.trackEvent('force_reread', relativePath, estimateTokens(contents));

package/dist/tools/force-reread.js.map

@@ -1 +1 @@
-{"version":3,"file":"force-reread.js","sourceRoot":"","sources":["../../src/tools/force-reread.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAC5C,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AACjC,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAC;AAChD,OAAO,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AAC/C,OAAO,EAAE,mBAAmB,EAAE,uBAAuB,EAAE,MAAM,yBAAyB,CAAC;AACvF,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAC3D,OAAO,EAAE,cAAc,EAAE,MAAM,wBAAwB,CAAC;AAExD,OAAO,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AAEzD,MAAM,CAAC,KAAK,UAAU,WAAW,CAC/B,WAAmB,EACnB,YAAoB;IAEpB,YAAY,GAAG,YAAY,CAAC,WAAW,EAAE,YAAY,CAAC,CAAC;IACvD,uBAAuB,CAAC,WAAW,CAAC,CAAC;IACrC,MAAM,YAAY,GAAG,IAAI,CAAC,WAAW,EAAE,YAAY,CAAC,CAAC;IACrD,MAAM,QAAQ,GAAG,MAAM,QAAQ,CAAC,YAAY,EAAE,OAAO,CAAC,CAAC;IACvD,MAAM,IAAI,GAAG,YAAY,CAAC,QAAQ,CAAC,CAAC;IACpC,MAAM,OAAO,GAAG,MAAM,mBAAmB,CAAC,WAAW,EAAE,YAAY,EAAE,QAAQ,CAAC,CAAC;IAE/E,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,WAAW,CAAC,CAAC;IAC1C,KAAK,CAAC,QAAQ,CAAC,YAAY,EAAE,IAAI,EAAE,OAAO,CAAC,CAAC;IAE5C,MAAM,OAAO,GAAG,IAAI,gBAAgB,CAAC,WAAW,CAAC,CAAC;IAClD,OAAO,CAAC,UAAU,CAAC,cAAc,EAAE,YAAY,EAAE,cAAc,CAAC,QAAQ,CAAC,CAAC,CAAC;IAE3E,OAAO,EAAE,IAAI,EAAE,YAAY,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,oCAAoC,EAAE,CAAC;AAC3G,CAAC"}
+{"version":3,"file":"force-reread.js","sourceRoot":"","sources":["../../src/tools/force-reread.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAC5C,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AACjC,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAC;AAChD,OAAO,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AAC/C,OAAO,EAAE,gBAAgB,EAAE,MAAM,iCAAiC,CAAC;AACnE,OAAO,EAAE,mBAAmB,EAAE,uBAAuB,EAAE,MAAM,yBAAyB,CAAC;AACvF,OAAO,EAAE,eAAe,EAAE,MAAM,8BAA8B,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAC3D,OAAO,EAAE,cAAc,EAAE,MAAM,wBAAwB,CAAC;AAExD,OAAO,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AAEzD,MAAM,CAAC,KAAK,UAAU,WAAW,CAC/B,WAAmB,EACnB,YAAoB;IAEpB,YAAY,GAAG,YAAY,CAAC,WAAW,EAAE,YAAY,CAAC,CAAC;IACvD,uBAAuB,CAAC,WAAW,CAAC,CAAC;IACrC,MAAM,YAAY,GAAG,IAAI,CAAC,WAAW,EAAE,YAAY,CAAC,CAAC;IACrD,MAAM,QAAQ,GAAG,MAAM,QAAQ,CAAC,YAAY,EAAE,OAAO,CAAC,CAAC;IACvD,MAAM,IAAI,GAAG,YAAY,CAAC,QAAQ,CAAC,CAAC;IACpC,MAAM,OAAO,GAAG,MAAM,mBAAmB,CAAC,WAAW,EAAE,YAAY,EAAE,QAAQ,CAAC,CAAC;IAE/E,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,WAAW,CAAC,CAAC;IAC1C,2EAA2E;IAC3E,6DAA6D;IAC7D,IAAI,gBAAgB,CAAC,YAAY,CAAC,EAAE,CAAC;QACnC,IAAI,eAAe,CAAC,WAAW,CAAC,CAAC,UAAU,CAAC,YAAY,EAAE,QAAQ,CAAC,CAAC;IACtE,CAAC;IACD,KAAK,CAAC,QAAQ,CAAC,YAAY,EAAE,IAAI,EAAE,OAAO,CAAC,CAAC;IAE5C,MAAM,OAAO,GAAG,IAAI,gBAAgB,CAAC,WAAW,CAAC,CAAC;IAClD,OAAO,CAAC,UAAU,CAAC,cAAc,EAAE,YAAY,EAAE,cAAc,CAAC,QAAQ,CAAC,CAAC,CAAC;IAE3E,OAAO,EAAE,IAAI,EAAE,YAAY,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,oCAAoC,EAAE,CAAC;AAC3G,CAAC"}

package/dist/tools/get-changed-files.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"get-changed-files.d.ts","sourceRoot":"","sources":["../../src/tools/get-changed-files.ts"],"names":[],"mappings":"AAKA,MAAM,WAAW,kBAAkB;IACjC,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,eAAe,CACnC,WAAW,EAAE,MAAM,EACnB,KAAK,CAAC,EAAE,MAAM,GACb,OAAO,CAAC,kBAAkB,CAAC,CAuD7B"}
+{"version":3,"file":"get-changed-files.d.ts","sourceRoot":"","sources":["../../src/tools/get-changed-files.ts"],"names":[],"mappings":"AAQA,MAAM,WAAW,kBAAkB;IACjC,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;CACnB;AAED,wBAAsB,eAAe,CACnC,WAAW,EAAE,MAAM,EACnB,KAAK,CAAC,EAAE,MAAM,GACb,OAAO,CAAC,kBAAkB,CAAC,CAsE7B"}

package/dist/tools/get-changed-files.js

@@ -1,6 +1,9 @@
+import { readFile } from 'node:fs/promises';
 import { join } from 'path';
 import { CacheStore } from '../cache/store.js';
-import { hashFile } from '../cache/hash.js';
+import { hashContents } from '../cache/hash.js';
+import { DependencyGraph } from '../graph/dependency-graph.js';
+import { isGraphIndexable } from '../indexer/source-extensions.js';
 import { scanProject } from '../indexer/scanner.js';
 export async function getChangedFiles(projectRoot, since) {
     const store = new CacheStore(projectRoot);
@@ -11,11 +14,17 @@ export async function getChangedFiles(projectRoot, since) {
     const sinceTimestamp = parseSince(since);
     const changed = [];
     const added = [];
+    const graph = new DependencyGraph(projectRoot);
     await Promise.all(scannedFiles.map(async (relativePath) => {
         const absolutePath = join(projectRoot, relativePath);
-        const currentHash = await hashFile(absolutePath);
-        if (!currentHash)
+        let contents;
+        try {
+            contents = await readFile(absolutePath, 'utf-8');
+        }
+        catch {
             return;
+        }
+        const currentHash = hashContents(contents);
         const cached = cachedByPath.get(relativePath);
         if (!cached) {
             added.push(relativePath);
@@ -25,8 +34,17 @@ export async function getChangedFiles(projectRoot, since) {
                 changed.push(relativePath);
             }
         }
-        // Update the cache entry with current hash and timestamp
-        store.setEntry(relativePath, currentHash, cached?.summary ?? null);
+        // Update the cache entry with current hash and timestamp. A summary may
+        // only be stored under the hash it was computed from — when the file
+        // changed, store null so the summary regenerates on next access instead
+        // of masquerading as a fresh cache hit. Import edges follow the same
+        // rule: recording a new hash without re-extracting edges would let the
+        // graph serve stale edges as fresh.
+        const summaryStillValid = cached !== undefined && cached.hash === currentHash;
+        if (!summaryStillValid && isGraphIndexable(relativePath)) {
+            graph.updateFile(relativePath, contents);
+        }
+        store.setEntry(relativePath, currentHash, summaryStillValid ? cached.summary : null);
     }));
     // Files in cache but not in scan are deleted
     const deleted = [];

package/dist/tools/get-changed-files.js.map

@@ -1 +1 @@
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package/dist/tools/get-dependency-graph.d.ts

@@ -1,17 +1,19 @@
 export interface DependencyGraphResult {
-    nodes: string[];
-    edges: Array<{
-        from: string;
-        to: string;
-    }>;
+    /** Adjacency map: file -> files it imports (present when direction includes dependencies). */
+    deps?: Record<string, string[]>;
+    /** Adjacency map: file -> files that import it (present when direction includes dependents). */
+    dependents?: Record<string, string[]>;
     stats: {
         totalFiles: number;
         totalEdges: number;
-        mostConnected: Array<{
+        /** Only present in the no-path whole-repo summary mode. */
+        mostConnected?: Array<{
             path: string;
             connections: number;
         }>;
     };
+    /** True when the no-path summary was capped by `limit`; stats carry whole-graph totals. */
+    truncated?: boolean;
 }
-export declare function getDependencyGraphTool(projectRoot: string, path?: string, direction?: 'dependencies' | 'dependents' | 'both', depth?: number, symbol?: string): Promise<DependencyGraphResult>;
+export declare function getDependencyGraphTool(projectRoot: string, path?: string, direction?: 'dependencies' | 'dependents' | 'both', depth?: number, symbol?: string, limit?: number): Promise<DependencyGraphResult>;
 //# sourceMappingURL=get-dependency-graph.d.ts.map

package/dist/tools/get-dependency-graph.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"get-dependency-graph.d.ts","sourceRoot":"","sources":["../../src/tools/get-dependency-graph.ts"],"names":[],"mappings":"AAOA,MAAM,WAAW,qBAAqB;IACpC,8FAA8F;IAC9F,IAAI,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC,CAAC;IAChC,gGAAgG;IAChG,UAAU,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC,CAAC;IACtC,KAAK,EAAE;QACL,UAAU,EAAE,MAAM,CAAC;QACnB,UAAU,EAAE,MAAM,CAAC;QACnB,2DAA2D;QAC3D,aAAa,CAAC,EAAE,KAAK,CAAC;YAAE,IAAI,EAAE,MAAM,CAAC;YAAC,WAAW,EAAE,MAAM,CAAA;SAAE,CAAC,CAAC;KAC9D,CAAC;IACF,2FAA2F;IAC3F,SAAS,CAAC,EAAE,OAAO,CAAC;CACrB;AAED,wBAAsB,sBAAsB,CAC1C,WAAW,EAAE,MAAM,EACnB,IAAI,CAAC,EAAE,MAAM,EACb,SAAS,CAAC,EAAE,cAAc,GAAG,YAAY,GAAG,MAAM,EAClD,KAAK,CAAC,EAAE,MAAM,EACd,MAAM,CAAC,EAAE,MAAM,EACf,KAAK,CAAC,EAAE,MAAM,GACb,OAAO,CAAC,qBAAqB,CAAC,CAgBhC"}