@blamechris/repo-memory 0.11.0 → 0.13.0

package/dist/cache/store.js

@@ -1,4 +1,24 @@
 import { getDatabase } from '../persistence/db.js';
+import { GENERATION_META_KEY, isStoredGenerationNewer } from './generation.js';
+const UPSERT_ENTRY = `INSERT INTO files (path, hash, last_checked, summary_json)
+   VALUES (?, ?, ?, ?)
+   ON CONFLICT(path) DO UPDATE SET
+     hash = excluded.hash,
+     last_checked = excluded.last_checked,
+     summary_json = excluded.summary_json`;
+/**
+ * Upsert used when a lower-generation process tried to write a summary
+ * (read-through mode): the hash and timestamp are persisted so change
+ * detection stays correct, but the summary is not — and a newer-generation
+ * summary already stored for the *same hash* is preserved rather than nulled.
+ * (`files.hash` in the CASE refers to the pre-update row value.)
+ */
+const UPSERT_ENTRY_WITHOUT_SUMMARY = `INSERT INTO files (path, hash, last_checked, summary_json)
+   VALUES (?, ?, ?, NULL)
+   ON CONFLICT(path) DO UPDATE SET
+     summary_json = CASE WHEN files.hash = excluded.hash THEN files.summary_json ELSE NULL END,
+     hash = excluded.hash,
+     last_checked = excluded.last_checked`;
 function rowToEntry(row) {
     return {
         path: row.path,
@@ -21,14 +41,27 @@ export class CacheStore {
     }
     setEntry(path, hash, summary) {
         const db = getDatabase(this.projectRoot);
-        const summaryJson = summary ? JSON.stringify(summary) : null;
         const now = Date.now();
-        db.prepare(`INSERT INTO files (path, hash, last_checked, summary_json)
-       VALUES (?, ?, ?, ?)
-       ON CONFLICT(path) DO UPDATE SET
-         hash = excluded.hash,
-         last_checked = excluded.last_checked,
-         summary_json = excluded.summary_json`).run(path, hash, now, summaryJson);
+        if (summary === null) {
+            // A single statement is already atomic, and a null summary is safe to
+            // write at any generation — no guard needed.
+            db.prepare(UPSERT_ENTRY).run(path, hash, now, null);
+            return;
+        }
+        // Summary writes re-check the stored generation tag every time (cheap
+        // single-row read) instead of trusting the per-process memoization in
+        // ensureSummaryGeneration: an external writer (e.g. a newer package
+        // version run by a post-merge hook) may have bumped the generation since
+        // this process last looked. BEGIN IMMEDIATE holds the write lock across
+        // the check and the write so the tag cannot change in between.
+        db.transaction(() => {
+            if (this.summaryWritesBlocked(db)) {
+                db.prepare(UPSERT_ENTRY_WITHOUT_SUMMARY).run(path, hash, now);
+            }
+            else {
+                db.prepare(UPSERT_ENTRY).run(path, hash, now, JSON.stringify(summary));
+            }
+        }).immediate();
     }
     getAllEntries() {
         const db = getDatabase(this.projectRoot);
@@ -37,26 +70,55 @@ export class CacheStore {
             .all();
         return rows.map(rowToEntry);
     }
+    /**
+     * Remove a cache entry and the dependency-graph edges extracted from it, in
+     * one transaction. Edges derive from the file's contents, so they share the
+     * entry's lifetime — leaving them behind would serve stale graph data until
+     * the next GC pass. (Incoming edges from other files are left alone: those
+     * files' contents still declare the import.)
+     */
     deleteEntry(path) {
         const db = getDatabase(this.projectRoot);
-        db.prepare('DELETE FROM files WHERE path = ?').run(path);
+        const remove = db.transaction((p) => {
+            db.prepare('DELETE FROM imports WHERE source = ?').run(p);
+            db.prepare('DELETE FROM files WHERE path = ?').run(p);
+        });
+        remove(path);
+    }
+    /** Refresh last_checked for an entry without altering its hash or summary. */
+    touchEntry(path) {
+        const db = getDatabase(this.projectRoot);
+        db.prepare('UPDATE files SET last_checked = ? WHERE path = ?').run(Date.now(), path);
     }
     setEntries(entries) {
         const db = getDatabase(this.projectRoot);
         const now = Date.now();
-        const stmt = db.prepare(`INSERT INTO files (path, hash, last_checked, summary_json)
-       VALUES (?, ?, ?, ?)
-       ON CONFLICT(path) DO UPDATE SET
-         hash = excluded.hash,
-         last_checked = excluded.last_checked,
-         summary_json = excluded.summary_json`);
-        const runBatch = db.transaction(() => {
+        const upsert = db.prepare(UPSERT_ENTRY);
+        const upsertWithoutSummary = db.prepare(UPSERT_ENTRY_WITHOUT_SUMMARY);
+        // IMMEDIATE so the generation check and the batch write happen under one
+        // uninterrupted write lock (see setEntry).
+        db.transaction(() => {
+            const blocked = this.summaryWritesBlocked(db);
             for (const entry of entries) {
-                const summaryJson = entry.summary ? JSON.stringify(entry.summary) : null;
-                stmt.run(entry.path, entry.hash, now, summaryJson);
+                if (entry.summary && blocked) {
+                    upsertWithoutSummary.run(entry.path, entry.hash, now);
+                }
+                else {
+                    const summaryJson = entry.summary ? JSON.stringify(entry.summary) : null;
+                    upsert.run(entry.path, entry.hash, now, summaryJson);
+                }
             }
-        });
-        runBatch();
+        }).immediate();
+    }
+    /**
+     * Whether the stored generation tag belongs to a strictly newer package
+     * generation than this process, in which case summary writes from this
+     * process must not be persisted (Guardian I3). Must be called while the
+     * write lock is held so the answer cannot change before the write lands.
+     */
+    summaryWritesBlocked(db) {
+        const row = db.prepare('SELECT value FROM meta WHERE key = ?').get(GENERATION_META_KEY);
+        return isStoredGenerationNewer(row?.value ?? null);
     }
     /** Read a value from the meta key/value table. */
     getMeta(key) {
@@ -79,6 +141,35 @@ export class CacheStore {
         const db = getDatabase(this.projectRoot);
         db.prepare('UPDATE files SET summary_json = NULL').run();
     }
+    /**
+     * Atomically drop all summaries and write a meta value in one IMMEDIATE
+     * transaction (Guardian I4). Used for generation bumps: no other process
+     * can insert an old-generation summary between the clear and the tag write,
+     * and a crash between the two is unobservable.
+     */
+    clearAllSummariesAndSetMeta(key, value) {
+        const db = getDatabase(this.projectRoot);
+        db.transaction(() => {
+            db.prepare('UPDATE files SET summary_json = NULL').run();
+            db.prepare(`INSERT INTO meta (key, value) VALUES (?, ?)
+         ON CONFLICT(key) DO UPDATE SET value = excluded.value`).run(key, value);
+        }).immediate();
+    }
+    /**
+     * Run `fn` while holding the database write lock (BEGIN IMMEDIATE). Use for
+     * read-decide-write sequences that must not interleave with writes from
+     * other processes. Nested store calls that open their own transactions
+     * collapse into savepoints inside this one.
+     */
+    withWriteLock(fn) {
+        const db = getDatabase(this.projectRoot);
+        return db.transaction(fn).immediate();
+    }
+    /** Delete every cache entry in a single atomic statement. */
+    deleteAllEntries() {
+        const db = getDatabase(this.projectRoot);
+        db.prepare('DELETE FROM files').run();
+    }
     getStaleEntries(maxAge) {
         const db = getDatabase(this.projectRoot);
         const cutoff = Date.now() - maxAge;

package/dist/cache/store.js.map

@@ -1 +1 @@
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package/dist/config.d.ts

@@ -6,7 +6,7 @@ export interface ToolGroupConfig {
 export interface RepoMemoryConfig {
     ignore?: string[];
     maxFiles?: number;
-    /** Summary engine for TS/JS files: 'regex' (default) or 'ast' (tree-sitter). */
+    /** Summary engine: 'ast' (default, tree-sitter) or 'regex'. */
     summarizer?: 'regex' | 'ast';
     gc?: {
         cacheMaxAgeDays?: number;

package/dist/config.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAKA,MAAM,WAAW,eAAe;IAC9B,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,SAAS,CAAC,EAAE,OAAO,CAAC;CACrB;AAED,MAAM,WAAW,gBAAgB;IAC/B,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,gFAAgF;IAChF,UAAU,CAAC,EAAE,OAAO,GAAG,KAAK,CAAC;IAC7B,EAAE,CAAC,EAAE;QACH,eAAe,CAAC,EAAE,MAAM,CAAC;QACzB,cAAc,CAAC,EAAE,MAAM,CAAC;QACxB,mBAAmB,CAAC,EAAE,MAAM,CAAC;KAC9B,CAAC;IACF,KAAK,CAAC,EAAE,eAAe,CAAC;CACzB;AAQD,wBAAgB,UAAU,CAAC,WAAW,EAAE,MAAM,GAAG,gBAAgB,CAqBhE;AAiFD,wBAAgB,gBAAgB,IAAI,IAAI,CAEvC"}
+{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAKA,MAAM,WAAW,eAAe;IAC9B,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,SAAS,CAAC,EAAE,OAAO,CAAC;CACrB;AAED,MAAM,WAAW,gBAAgB;IAC/B,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,+DAA+D;IAC/D,UAAU,CAAC,EAAE,OAAO,GAAG,KAAK,CAAC;IAC7B,EAAE,CAAC,EAAE;QACH,eAAe,CAAC,EAAE,MAAM,CAAC;QACzB,cAAc,CAAC,EAAE,MAAM,CAAC;QACxB,mBAAmB,CAAC,EAAE,MAAM,CAAC;KAC9B,CAAC;IACF,KAAK,CAAC,EAAE,eAAe,CAAC;CACzB;AAQD,wBAAgB,UAAU,CAAC,WAAW,EAAE,MAAM,GAAG,gBAAgB,CAqBhE;AAiFD,wBAAgB,gBAAgB,IAAI,IAAI,CAEvC"}

package/dist/graph/dependency-graph.d.ts

@@ -7,6 +7,18 @@ export declare class DependencyGraph {
     load(): void;
     /** Update edges for a single file (incremental). */
     updateFile(filePath: string, contents: string): void;
+    /**
+     * Remove a file from the graph entirely: every persisted edge where it is
+     * the source or the target, plus the in-memory adjacency for both
+     * directions. Used when a file no longer exists on disk.
+     */
+    removeFile(filePath: string): void;
+    /**
+     * Remove every graph node (and its edges, in both directions) that is not
+     * in the given set of existing files. Call after load() so the in-memory
+     * maps reflect the persisted state.
+     */
+    prune(existingFiles: ReadonlySet<string>): void;
     /** Get direct dependencies of a file. */
     getDependencies(path: string): string[];
     /** Get direct dependents of a file. */
@@ -26,6 +38,8 @@ export declare class DependencyGraph {
         path: string;
         connections: number;
     }>;
+    /** Drop a node from the in-memory adjacency maps, in both directions. */
+    private removeNode;
     private addEdge;
     private bfs;
 }

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

@@ -1 +1 @@
-{"version":3,"file":"dependency-graph.d.ts","sourceRoot":"","sources":["../../src/graph/dependency-graph.ts"],"names":[],"mappings":"AAGA,qBAAa,eAAe;IAC1B,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAS;IACrC,OAAO,CAAC,QAAQ,CAA2B;IAC3C,OAAO,CAAC,QAAQ,CAA2B;gBAE/B,WAAW,EAAE,MAAM;IAM/B,wDAAwD;IACxD,IAAI,IAAI,IAAI;IAcZ,oDAAoD;IACpD,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,IAAI;IAuCpD,yCAAyC;IACzC,eAAe,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,EAAE;IAKvC,uCAAuC;IACvC,aAAa,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,EAAE;IAKrC,2DAA2D;IAC3D,gBAAgB,CAAC,MAAM,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,MAAM,GAAG,KAAK,CAAC;QAAE,MAAM,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAC;QAAC,UAAU,EAAE,MAAM,EAAE,CAAA;KAAE,CAAC;IAwBtH,uEAAuE;IACvE,yBAAyB,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE;IAIpE,qEAAqE;IACrE,uBAAuB,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE;IAIlE,sEAAsE;IACtE,gBAAgB,CAAC,KAAK,GAAE,MAAW,GAAG,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,WAAW,EAAE,MAAM,CAAA;KAAE,CAAC;IAgBlF,OAAO,CAAC,OAAO;IAgBf,OAAO,CAAC,GAAG;CAkCZ"}
+{"version":3,"file":"dependency-graph.d.ts","sourceRoot":"","sources":["../../src/graph/dependency-graph.ts"],"names":[],"mappings":"AAGA,qBAAa,eAAe;IAC1B,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAS;IACrC,OAAO,CAAC,QAAQ,CAA2B;IAC3C,OAAO,CAAC,QAAQ,CAA2B;gBAE/B,WAAW,EAAE,MAAM;IAM/B,wDAAwD;IACxD,IAAI,IAAI,IAAI;IAcZ,oDAAoD;IACpD,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,IAAI;IA0CpD;;;;OAIG;IACH,UAAU,CAAC,QAAQ,EAAE,MAAM,GAAG,IAAI;IAUlC;;;;OAIG;IACH,KAAK,CAAC,aAAa,EAAE,WAAW,CAAC,MAAM,CAAC,GAAG,IAAI;IAa/C,yCAAyC;IACzC,eAAe,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,EAAE;IAKvC,uCAAuC;IACvC,aAAa,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,EAAE;IAKrC,2DAA2D;IAC3D,gBAAgB,CAAC,MAAM,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,MAAM,GAAG,KAAK,CAAC;QAAE,MAAM,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAC;QAAC,UAAU,EAAE,MAAM,EAAE,CAAA;KAAE,CAAC;IAwBtH,uEAAuE;IACvE,yBAAyB,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE;IAIpE,qEAAqE;IACrE,uBAAuB,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE;IAIlE,sEAAsE;IACtE,gBAAgB,CAAC,KAAK,GAAE,MAAW,GAAG,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,WAAW,EAAE,MAAM,CAAA;KAAE,CAAC;IAgBlF,yEAAyE;IACzE,OAAO,CAAC,UAAU;IA0BlB,OAAO,CAAC,OAAO;IAgBf,OAAO,CAAC,GAAG;CAkCZ"}

package/dist/graph/dependency-graph.js

@@ -38,19 +38,57 @@ export class DependencyGraph {
             }
             this.outgoing.delete(filePath);
         }
-        // Delete old rows from DB
-        db.prepare('DELETE FROM imports WHERE source = ?').run(filePath);
         // Extract new imports
         const imports = extractImports(filePath, contents, this.projectRoot);
-        // Insert new rows and update in-memory maps
         const insert = db.prepare('INSERT OR REPLACE INTO imports (source, target, specifiers, import_type) VALUES (?, ?, ?, ?)');
-        const insertAll = db.transaction(() => {
+        // Delete + insert in ONE transaction so concurrent readers never observe a
+        // torn state where the file's old edges are gone but the new ones are not
+        // yet written (audit invariant I2).
+        const replaceAll = db.transaction(() => {
+            db.prepare('DELETE FROM imports WHERE source = ?').run(filePath);
             for (const ref of imports) {
+                // External targets (bare modules, builtins, unresolvable paths) are not
+                // repo files — persisting them would pollute traversal and mostConnected.
+                if (ref.external)
+                    continue;
                 insert.run(ref.source, ref.target, JSON.stringify(ref.specifiers), ref.type);
                 this.addEdge(ref.source, ref.target);
             }
         });
-        insertAll();
+        replaceAll();
+    }
+    /**
+     * Remove a file from the graph entirely: every persisted edge where it is
+     * the source or the target, plus the in-memory adjacency for both
+     * directions. Used when a file no longer exists on disk.
+     */
+    removeFile(filePath) {
+        const db = getDatabase(this.projectRoot);
+        const remove = db.transaction(() => {
+            db.prepare('DELETE FROM imports WHERE source = ?').run(filePath);
+            db.prepare('DELETE FROM imports WHERE target = ?').run(filePath);
+        });
+        remove();
+        this.removeNode(filePath);
+    }
+    /**
+     * Remove every graph node (and its edges, in both directions) that is not
+     * in the given set of existing files. Call after load() so the in-memory
+     * maps reflect the persisted state.
+     */
+    prune(existingFiles) {
+        const missing = new Set();
+        for (const node of this.outgoing.keys()) {
+            if (!existingFiles.has(node))
+                missing.add(node);
+        }
+        for (const node of this.incoming.keys()) {
+            if (!existingFiles.has(node))
+                missing.add(node);
+        }
+        for (const node of missing) {
+            this.removeFile(node);
+        }
     }
     /** Get direct dependencies of a file. */
     getDependencies(path) {
@@ -109,6 +147,33 @@ export class DependencyGraph {
         result.sort((a, b) => b.connections - a.connections);
         return result.slice(0, limit);
     }
+    /** Drop a node from the in-memory adjacency maps, in both directions. */
+    removeNode(node) {
+        const targets = this.outgoing.get(node);
+        if (targets) {
+            for (const target of targets) {
+                const sources = this.incoming.get(target);
+                if (sources) {
+                    sources.delete(node);
+                    if (sources.size === 0)
+                        this.incoming.delete(target);
+                }
+            }
+            this.outgoing.delete(node);
+        }
+        const sources = this.incoming.get(node);
+        if (sources) {
+            for (const source of sources) {
+                const targets = this.outgoing.get(source);
+                if (targets) {
+                    targets.delete(node);
+                    if (targets.size === 0)
+                        this.outgoing.delete(source);
+                }
+            }
+            this.incoming.delete(node);
+        }
+    }
     addEdge(source, target) {
         let targets = this.outgoing.get(source);
         if (!targets) {

package/dist/graph/dependency-graph.js.map

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package/dist/graph/refresh.d.ts

@@ -0,0 +1,21 @@
+import { DependencyGraph } from './dependency-graph.js';
+/**
+ * Load the persisted dependency graph and bring it up to date without
+ * re-reading unchanged files.
+ *
+ * Freshness strategy:
+ * 1. `load()` the persisted edges, then prune nodes whose files are gone from
+ *    the project file list.
+ * 2. For each graph-indexable file, `stat` it (cheap, no content read). If a
+ *    `files` row exists and the mtime predates the row's `last_checked`, the
+ *    content cannot have changed since the stored hash was computed — skip.
+ * 3. Otherwise read the file once, hash it, and compare with the stored hash:
+ *    only a real change (or a missing row) re-extracts edges. Edge writes and
+ *    summary-cache rows share the same hash bookkeeping, so edges have the
+ *    same freshness semantics as summaries (never-stale invariant).
+ *
+ * @param scannedFiles Optional pre-scanned project file list (avoids a second
+ *   scan when the caller already has one).
+ */
+export declare function loadFreshGraph(projectRoot: string, scannedFiles?: string[]): Promise<DependencyGraph>;
+//# sourceMappingURL=refresh.d.ts.map

package/dist/graph/refresh.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"refresh.d.ts","sourceRoot":"","sources":["../../src/graph/refresh.ts"],"names":[],"mappings":"AAMA,OAAO,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAC;AAoBxD;;;;;;;;;;;;;;;;;GAiBG;AACH,wBAAsB,cAAc,CAClC,WAAW,EAAE,MAAM,EACnB,YAAY,CAAC,EAAE,MAAM,EAAE,GACtB,OAAO,CAAC,eAAe,CAAC,CA8D1B"}

package/dist/graph/refresh.js

@@ -0,0 +1,101 @@
+import { readFile, stat } from 'node:fs/promises';
+import { join } from 'node:path';
+import { hashContents } from '../cache/hash.js';
+import { CacheStore } from '../cache/store.js';
+import { scanProject } from '../indexer/scanner.js';
+import { isGraphIndexable } from '../indexer/source-extensions.js';
+import { DependencyGraph } from './dependency-graph.js';
+/**
+ * Meta key recording that the persisted graph has been fully built at least
+ * once by this implementation. Caches created before the graph was wired into
+ * the write path have file rows but no edges — without this marker those
+ * files would look "fresh" forever and never get indexed. Bump the value to
+ * force a one-time full re-extraction after a change to the edge format.
+ */
+const GRAPH_GENERATION_KEY = 'graph_generation';
+const GRAPH_GENERATION = '1';
+/**
+ * Filesystem mtimes can be coarser than Date.now() (whole-second granularity
+ * on some filesystems), so an edit made just after a check can carry an mtime
+ * that is *truncated below* the stored last_checked. Files whose mtime falls
+ * within this window of last_checked stay suspect and get hash-checked.
+ */
+const MTIME_SAFETY_WINDOW_MS = 2000;
+/**
+ * Load the persisted dependency graph and bring it up to date without
+ * re-reading unchanged files.
+ *
+ * Freshness strategy:
+ * 1. `load()` the persisted edges, then prune nodes whose files are gone from
+ *    the project file list.
+ * 2. For each graph-indexable file, `stat` it (cheap, no content read). If a
+ *    `files` row exists and the mtime predates the row's `last_checked`, the
+ *    content cannot have changed since the stored hash was computed — skip.
+ * 3. Otherwise read the file once, hash it, and compare with the stored hash:
+ *    only a real change (or a missing row) re-extracts edges. Edge writes and
+ *    summary-cache rows share the same hash bookkeeping, so edges have the
+ *    same freshness semantics as summaries (never-stale invariant).
+ *
+ * @param scannedFiles Optional pre-scanned project file list (avoids a second
+ *   scan when the caller already has one).
+ */
+export async function loadFreshGraph(projectRoot, scannedFiles) {
+    const files = scannedFiles ?? (await scanProject(projectRoot));
+    const store = new CacheStore(projectRoot);
+    const graph = new DependencyGraph(projectRoot);
+    graph.load();
+    // Legacy caches (or a bumped edge format) need one full re-extraction pass.
+    const fullRebuild = store.getMeta(GRAPH_GENERATION_KEY) !== GRAPH_GENERATION;
+    // Files that left the project take their edges with them. (Files still in
+    // the git index but deleted from disk are caught by the stat pass below.)
+    graph.prune(new Set(files));
+    for (const file of files) {
+        if (!isGraphIndexable(file))
+            continue;
+        const absolutePath = join(projectRoot, file);
+        let mtimeMs;
+        try {
+            mtimeMs = (await stat(absolutePath)).mtimeMs;
+        }
+        catch {
+            // Tracked in git but missing on disk (or deleted mid-pass): the file
+            // does not exist anymore, so its edges must not be served.
+            graph.removeFile(file);
+            continue;
+        }
+        const entry = store.getEntry(file);
+        if (!fullRebuild && entry && mtimeMs < entry.lastChecked - MTIME_SAFETY_WINDOW_MS) {
+            // Unmodified since the stored hash was computed — do not re-read.
+            continue;
+        }
+        let contents;
+        try {
+            contents = await readFile(absolutePath, 'utf-8');
+        }
+        catch {
+            graph.removeFile(file);
+            continue;
+        }
+        const currentHash = hashContents(contents);
+        if (entry && entry.hash === currentHash) {
+            // Content unchanged; edges for this hash are already persisted (unless
+            // this is the one-time full rebuild). Bump last_checked so the next
+            // pass can skip on mtime alone once the file ages past the safety window.
+            if (fullRebuild)
+                graph.updateFile(file, contents);
+            store.touchEntry(file);
+        }
+        else {
+            graph.updateFile(file, contents);
+            // Record the hash the edges were extracted from. A pre-existing summary
+            // was computed from different content, so it must not survive the hash
+            // update (same rule as the summary cache itself).
+            store.setEntry(file, currentHash, null);
+        }
+    }
+    if (fullRebuild) {
+        store.setMeta(GRAPH_GENERATION_KEY, GRAPH_GENERATION);
+    }
+    return graph;
+}
+//# sourceMappingURL=refresh.js.map

package/dist/graph/refresh.js.map

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