@optave/codegraph 3.9.3 → 3.9.5

package/dist/domain/graph/builder/stages/finalize.js

@@ -3,6 +3,7 @@
  *
  * WASM cleanup, stats logging, drift detection, build metadata, registry, journal.
  */
+import fs from 'node:fs';
 import { tmpdir } from 'node:os';
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
@@ -62,27 +63,49 @@ function persistBuildMetadata(ctx, nodeCount, actualEdgeCount, buildNow) {
     const useNativeDb = ctx.engineName === 'native' && !!ctx.nativeDb;
     if (!ctx.isFullBuild && ctx.allSymbols.size <= 3)
         return;
+    // When the native engine is active, persist the Rust addon version so that
+    // checkEngineSchemaMismatch compares against the same value on the next build.
+    // Writing CODEGRAPH_VERSION (the npm package version) here would create a
+    // permanent mismatch whenever npm and crate versions diverge, forcing every
+    // subsequent build to be a full rebuild.
+    const codeVersionToWrite = ctx.engineName === 'native' && ctx.engineVersion ? ctx.engineVersion : CODEGRAPH_VERSION;
+    // Persist the repo root so downstream commands (e.g. `codegraph embed`)
+    // can resolve relative file paths regardless of the invoking cwd.
+    // Use realpathSync (symlink-resolving) to match the Rust engine's
+    // std::fs::canonicalize — otherwise the JS write here would overwrite the
+    // canonical path Rust wrote for native full builds and could re-introduce
+    // a non-canonical path when the project root is behind a symlink.
+    const resolvedRootDir = path.resolve(ctx.rootDir);
+    let rootDirToWrite = resolvedRootDir;
+    try {
+        rootDirToWrite = fs.realpathSync(resolvedRootDir);
+    }
+    catch {
+        /* realpath can fail (e.g. path no longer exists); fall back to resolve() */
+    }
     try {
         if (useNativeDb) {
             ctx.nativeDb.setBuildMeta(Object.entries({
                 engine: ctx.engineName,
-                engine_version: CODEGRAPH_VERSION,
-                codegraph_version: CODEGRAPH_VERSION,
+                engine_version: codeVersionToWrite,
+                codegraph_version: codeVersionToWrite,
                 schema_version: String(ctx.schemaVersion),
                 built_at: buildNow.toISOString(),
                 node_count: String(nodeCount),
                 edge_count: String(actualEdgeCount),
+                root_dir: rootDirToWrite,
             }).map(([key, value]) => ({ key, value: String(value) })));
         }
         else {
             setBuildMeta(ctx.db, {
                 engine: ctx.engineName,
-                engine_version: CODEGRAPH_VERSION,
-                codegraph_version: CODEGRAPH_VERSION,
+                engine_version: codeVersionToWrite,
+                codegraph_version: codeVersionToWrite,
                 schema_version: String(ctx.schemaVersion),
                 built_at: buildNow.toISOString(),
                 node_count: nodeCount,
                 edge_count: actualEdgeCount,
+                root_dir: rootDirToWrite,
             });
         }
     }

package/dist/domain/graph/builder/stages/finalize.js.map

@@ -1 +1 @@
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package/dist/domain/graph/builder/stages/run-analyses.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"run-analyses.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/run-analyses.ts"],"names":[],"mappings":"AAQA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAErD,wBAAsB,WAAW,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAoCrE"}
+{"version":3,"file":"run-analyses.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/run-analyses.ts"],"names":[],"mappings":"AAQA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAErD,wBAAsB,WAAW,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAerE"}

package/dist/domain/graph/builder/stages/run-analyses.js

@@ -2,30 +2,15 @@
  * Stage: runAnalyses
  *
  * Dispatches to the unified AST analysis engine (AST nodes, complexity, CFG, dataflow).
- * Filters out reverse-dep files for incremental builds.
+ * Reverse-dep files are no longer in allSymbols (they are not reparsed since #932/#933),
+ * so no filtering is needed here.
  */
-import { debug, warn } from '../../../../infrastructure/logger.js';
+import { warn } from '../../../../infrastructure/logger.js';
 export async function runAnalyses(ctx) {
-    const { db, allSymbols, rootDir, opts, engineOpts, isFullBuild, filesToParse } = ctx;
-    // For incremental builds, exclude reverse-dep-only files
-    let astComplexitySymbols = allSymbols;
-    if (!isFullBuild) {
-        const reverseDepFiles = new Set(filesToParse
-            .filter((item) => item._reverseDepOnly)
-            .map((item) => item.relPath));
-        if (reverseDepFiles.size > 0) {
-            astComplexitySymbols = new Map();
-            for (const [relPath, symbols] of allSymbols) {
-                if (!reverseDepFiles.has(relPath)) {
-                    astComplexitySymbols.set(relPath, symbols);
-                }
-            }
-            debug(`AST/complexity/CFG/dataflow: processing ${astComplexitySymbols.size} changed files (skipping ${reverseDepFiles.size} reverse-deps)`);
-        }
-    }
+    const { db, allSymbols, rootDir, opts, engineOpts } = ctx;
     const { runAnalyses: runAnalysesFn } = await import('../../../../ast-analysis/engine.js');
     try {
-        const analysisTiming = await runAnalysesFn(db, astComplexitySymbols, rootDir, opts, engineOpts);
+        const analysisTiming = await runAnalysesFn(db, allSymbols, rootDir, opts, engineOpts);
         ctx.timing.astMs = analysisTiming.astMs;
         ctx.timing.complexityMs = analysisTiming.complexityMs;
         ctx.timing.cfgMs = analysisTiming.cfgMs;

package/dist/domain/graph/builder/stages/run-analyses.js.map

@@ -1 +1 @@
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package/dist/domain/graph/journal.d.ts

@@ -11,5 +11,20 @@ export declare function appendJournalEntries(rootDir: string, entries: Array<{
     deleted?: boolean;
 }>): void;
 export declare function writeJournalHeader(rootDir: string, timestamp: number): void;
+/**
+ * Atomically append entries while advancing the header timestamp.
+ *
+ * Used by the watcher: without this, the header timestamp stays frozen at the
+ * last build's finalize time while entries accumulate, so the next build's
+ * Tier 0 check sees `journal.timestamp < MAX(file_hashes.mtime)`, rejects the
+ * journal, and falls through to the expensive mtime+size / hash scan.
+ *
+ * Writes a tmp file then renames — a crash mid-rename leaves the previous
+ * journal state intact.
+ */
+export declare function appendJournalEntriesAndStampHeader(rootDir: string, entries: Array<{
+    file: string;
+    deleted?: boolean;
+}>, timestamp: number): void;
 export {};
 //# sourceMappingURL=journal.d.ts.map

package/dist/domain/graph/journal.d.ts.map

@@ -1 +1 @@
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package/dist/domain/graph/journal.js

@@ -1,8 +1,222 @@
+import crypto from 'node:crypto';
 import fs from 'node:fs';
 import path from 'node:path';
 import { debug, warn } from '../../infrastructure/logger.js';
 export const JOURNAL_FILENAME = 'changes.journal';
 const HEADER_PREFIX = '# codegraph-journal v1 ';
+const LOCK_SUFFIX = '.lock';
+const LOCK_TIMEOUT_MS = 5_000;
+const LOCK_STALE_MS = 30_000;
+const LOCK_RETRY_MS = 25;
+// Busy-spin sleep avoids blocking the Node.js event loop (unlike Atomics.wait,
+// which freezes all I/O and timer callbacks). The retry interval is short
+// (25ms), so the CPU cost is negligible while keeping unrelated callbacks
+// responsive in watcher processes.
+function sleepSync(ms) {
+    const end = process.hrtime.bigint() + BigInt(ms) * 1000000n;
+    while (process.hrtime.bigint() < end) {
+        /* spin */
+    }
+}
+function isPidAlive(pid) {
+    if (!Number.isFinite(pid) || pid <= 0)
+        return false;
+    try {
+        process.kill(pid, 0);
+        return true;
+    }
+    catch (e) {
+        // EPERM means the process exists but we lack permission — still alive.
+        return e.code === 'EPERM';
+    }
+}
+/**
+ * Steal a stale lockfile atomically via write-tmp + rename.
+ *
+ * Using rename (which is atomic on POSIX and Windows) avoids the TOCTOU race
+ * inherent to the unlink + openSync('wx') pattern: if two stealers both
+ * observed the same stale holder, one's unlink could cross the other's fresh
+ * acquisition, admitting two writers into the critical section.
+ *
+ * After rename, we re-read the lockfile to confirm our nonce — if another
+ * stealer's rename landed after ours, they own the lock and we retry.
+ */
+function trySteal(lockPath) {
+    const nonce = `${process.pid}-${crypto.randomBytes(8).toString('hex')}`;
+    const tmpPath = `${lockPath}.${nonce}.tmp`;
+    try {
+        fs.writeFileSync(tmpPath, `${process.pid}\n${nonce}\n`, { flag: 'w' });
+    }
+    catch {
+        return null;
+    }
+    try {
+        // Atomic replace: overwrites the stale lockfile.
+        fs.renameSync(tmpPath, lockPath);
+    }
+    catch {
+        try {
+            fs.unlinkSync(tmpPath);
+        }
+        catch {
+            /* ignore */
+        }
+        return null;
+    }
+    // Verify the nonce — another stealer's rename may have landed after ours.
+    let content;
+    try {
+        content = fs.readFileSync(lockPath, 'utf-8');
+    }
+    catch {
+        return null;
+    }
+    if (!content.includes(nonce)) {
+        // Lost the race to another stealer; do NOT unlink their live lockfile.
+        return null;
+    }
+    let fd;
+    try {
+        // Re-open r+ so we have a persistent fd the caller can close on release.
+        fd = fs.openSync(lockPath, 'r+');
+    }
+    catch {
+        return null;
+    }
+    return { fd, nonce };
+}
+function acquireJournalLock(lockPath) {
+    const start = Date.now();
+    for (;;) {
+        const nonce = `${process.pid}-${crypto.randomBytes(8).toString('hex')}`;
+        try {
+            const fd = fs.openSync(lockPath, 'wx');
+            try {
+                fs.writeSync(fd, `${process.pid}\n${nonce}\n`);
+            }
+            catch {
+                // Stamp write failed (ENOSPC, I/O error). An empty lockfile would
+                // look stale to concurrent waiters (Number('') === 0, isPidAlive(0)
+                // returns false), so they'd steal our live lock. Release and retry.
+                try {
+                    fs.closeSync(fd);
+                }
+                catch {
+                    /* ignore */
+                }
+                try {
+                    fs.unlinkSync(lockPath);
+                }
+                catch {
+                    /* ignore */
+                }
+                if (Date.now() - start > LOCK_TIMEOUT_MS) {
+                    throw new Error(`Failed to acquire journal lock at ${lockPath} within ${LOCK_TIMEOUT_MS}ms`);
+                }
+                sleepSync(LOCK_RETRY_MS);
+                continue;
+            }
+            return { fd, nonce };
+        }
+        catch (e) {
+            if (e.code !== 'EEXIST')
+                throw e;
+        }
+        let holderAlive = true;
+        try {
+            const pidContent = fs.readFileSync(lockPath, 'utf-8').split('\n')[0].trim();
+            holderAlive = isPidAlive(Number(pidContent));
+        }
+        catch {
+            /* unreadable — fall through to age check */
+        }
+        let shouldSteal = !holderAlive;
+        if (holderAlive) {
+            try {
+                const stat = fs.statSync(lockPath);
+                if (Date.now() - stat.mtimeMs > LOCK_STALE_MS) {
+                    shouldSteal = true;
+                }
+            }
+            catch {
+                /* stat failed — keep retrying */
+            }
+        }
+        if (shouldSteal) {
+            const stolen = trySteal(lockPath);
+            if (stolen)
+                return stolen;
+            // Steal failed or lost the race — fall through to timeout check & retry.
+        }
+        if (Date.now() - start > LOCK_TIMEOUT_MS) {
+            throw new Error(`Failed to acquire journal lock at ${lockPath} within ${LOCK_TIMEOUT_MS}ms`);
+        }
+        sleepSync(LOCK_RETRY_MS);
+    }
+}
+function releaseJournalLock(lockPath, lock) {
+    try {
+        fs.closeSync(lock.fd);
+    }
+    catch {
+        /* ignore */
+    }
+    // Only unlink if the lockfile still carries our nonce — if another stealer
+    // decided we were stale and replaced it, we must not unlink their live lock.
+    try {
+        const content = fs.readFileSync(lockPath, 'utf-8');
+        if (content.includes(lock.nonce)) {
+            fs.unlinkSync(lockPath);
+        }
+    }
+    catch {
+        /* lockfile gone or unreadable — nothing to unlink */
+    }
+}
+function sweepStaleTmpFiles(dir) {
+    // Clean up orphaned .tmp files left behind when a process is killed after
+    // writeFileSync(tmpPath, ...) succeeds but before renameSync(tmpPath, lockPath)
+    // completes (trySteal path). Without this, tmp files accumulate silently in
+    // .codegraph/ across crash cycles. Only sweep ones older than LOCK_STALE_MS
+    // so we don't race an in-flight steal on another process.
+    let entries;
+    try {
+        entries = fs.readdirSync(dir, { withFileTypes: true });
+    }
+    catch {
+        return;
+    }
+    const now = Date.now();
+    const prefix = `${JOURNAL_FILENAME}${LOCK_SUFFIX}.`;
+    for (const entry of entries) {
+        if (!entry.isFile() || !entry.name.startsWith(prefix) || !entry.name.endsWith('.tmp')) {
+            continue;
+        }
+        const tmpPath = path.join(dir, entry.name);
+        try {
+            const stat = fs.statSync(tmpPath);
+            if (now - stat.mtimeMs > LOCK_STALE_MS) {
+                fs.unlinkSync(tmpPath);
+            }
+        }
+        catch {
+            /* stat/unlink raced another cleaner or was already removed — ignore */
+        }
+    }
+}
+function withJournalLock(rootDir, fn) {
+    const dir = path.join(rootDir, '.codegraph');
+    fs.mkdirSync(dir, { recursive: true });
+    sweepStaleTmpFiles(dir);
+    const lockPath = path.join(dir, `${JOURNAL_FILENAME}${LOCK_SUFFIX}`);
+    const lock = acquireJournalLock(lockPath);
+    try {
+        return fn();
+    }
+    finally {
+        releaseJournalLock(lockPath, lock);
+    }
+}
 export function readJournal(rootDir) {
     const journalPath = path.join(rootDir, '.codegraph', JOURNAL_FILENAME);
     let content;
@@ -47,40 +261,81 @@ export function readJournal(rootDir) {
     return { valid: true, timestamp, changed, removed };
 }
 export function appendJournalEntries(rootDir, entries) {
-    const dir = path.join(rootDir, '.codegraph');
-    const journalPath = path.join(dir, JOURNAL_FILENAME);
-    if (!fs.existsSync(dir)) {
-        fs.mkdirSync(dir, { recursive: true });
-    }
-    if (!fs.existsSync(journalPath)) {
-        fs.writeFileSync(journalPath, `${HEADER_PREFIX}0\n`);
-    }
-    const lines = entries.map((e) => {
-        if (e.deleted)
-            return `DELETED ${e.file}`;
-        return e.file;
+    withJournalLock(rootDir, () => {
+        const journalPath = path.join(rootDir, '.codegraph', JOURNAL_FILENAME);
+        if (!fs.existsSync(journalPath)) {
+            fs.writeFileSync(journalPath, `${HEADER_PREFIX}0\n`);
+        }
+        const lines = entries.map((e) => {
+            if (e.deleted)
+                return `DELETED ${e.file}`;
+            return e.file;
+        });
+        fs.appendFileSync(journalPath, `${lines.join('\n')}\n`);
     });
-    fs.appendFileSync(journalPath, `${lines.join('\n')}\n`);
 }
 export function writeJournalHeader(rootDir, timestamp) {
-    const dir = path.join(rootDir, '.codegraph');
-    const journalPath = path.join(dir, JOURNAL_FILENAME);
-    const tmpPath = `${journalPath}.tmp`;
-    if (!fs.existsSync(dir)) {
-        fs.mkdirSync(dir, { recursive: true });
-    }
-    try {
-        fs.writeFileSync(tmpPath, `${HEADER_PREFIX}${timestamp}\n`);
-        fs.renameSync(tmpPath, journalPath);
-    }
-    catch (err) {
-        warn(`Failed to write journal header: ${err.message}`);
+    withJournalLock(rootDir, () => {
+        const journalPath = path.join(rootDir, '.codegraph', JOURNAL_FILENAME);
+        const tmpPath = `${journalPath}.tmp`;
         try {
-            fs.unlinkSync(tmpPath);
+            fs.writeFileSync(tmpPath, `${HEADER_PREFIX}${timestamp}\n`);
+            fs.renameSync(tmpPath, journalPath);
+        }
+        catch (err) {
+            warn(`Failed to write journal header: ${err.message}`);
+            try {
+                fs.unlinkSync(tmpPath);
+            }
+            catch {
+                /* ignore */
+            }
+        }
+    });
+}
+/**
+ * Atomically append entries while advancing the header timestamp.
+ *
+ * Used by the watcher: without this, the header timestamp stays frozen at the
+ * last build's finalize time while entries accumulate, so the next build's
+ * Tier 0 check sees `journal.timestamp < MAX(file_hashes.mtime)`, rejects the
+ * journal, and falls through to the expensive mtime+size / hash scan.
+ *
+ * Writes a tmp file then renames — a crash mid-rename leaves the previous
+ * journal state intact.
+ */
+export function appendJournalEntriesAndStampHeader(rootDir, entries, timestamp) {
+    withJournalLock(rootDir, () => {
+        const journalPath = path.join(rootDir, '.codegraph', JOURNAL_FILENAME);
+        const tmpPath = `${journalPath}.tmp`;
+        let existingBody = '';
+        try {
+            const content = fs.readFileSync(journalPath, 'utf-8');
+            const newlineIdx = content.indexOf('\n');
+            if (newlineIdx >= 0)
+                existingBody = content.slice(newlineIdx + 1);
         }
         catch {
-            /* ignore */
+            /* no existing journal — fall through to write header + new entries */
         }
-    }
+        if (existingBody && !existingBody.endsWith('\n'))
+            existingBody = `${existingBody}\n`;
+        const newLines = entries.map((e) => (e.deleted ? `DELETED ${e.file}` : e.file));
+        const appended = newLines.length > 0 ? `${newLines.join('\n')}\n` : '';
+        const content = `${HEADER_PREFIX}${timestamp}\n${existingBody}${appended}`;
+        try {
+            fs.writeFileSync(tmpPath, content);
+            fs.renameSync(tmpPath, journalPath);
+        }
+        catch (err) {
+            warn(`Failed to update journal: ${err.message}`);
+            try {
+                fs.unlinkSync(tmpPath);
+            }
+            catch {
+                /* ignore */
+            }
+        }
+    });
 }
 //# sourceMappingURL=journal.js.map

package/dist/domain/graph/journal.js.map

@@ -1 +1 @@
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package/dist/domain/graph/watcher.d.ts

@@ -1,6 +1,23 @@
+/**
+ * Build journal entries for a pending-path set, detecting deletions by
+ * existence check.
+ *
+ * `ctx.pending` is an untyped `Set<string>` — it carries no event-type
+ * metadata. Without this check, a file deleted during the watch session
+ * would be journaled as "changed", causing the next incremental build to
+ * try to re-parse a non-existent file instead of removing it from the graph.
+ * Mirrors the deletion detection in `rebuildFile` (see builder/incremental.ts).
+ *
+ * Exported for unit-testing; prefer `setupShutdownHandler` in production paths.
+ */
+export declare function buildFlushEntriesFromPending(rootDir: string, pending: Iterable<string>): Array<{
+    file: string;
+    deleted: boolean;
+}>;
 export declare function watchProject(rootDir: string, opts?: {
     engine?: string;
     poll?: boolean;
     pollInterval?: number;
+    dbPath?: string;
 }): Promise<void>;
 //# sourceMappingURL=watcher.d.ts.map

package/dist/domain/graph/watcher.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"watcher.d.ts","sourceRoot":"","sources":["../../../src/domain/graph/watcher.ts"],"names":[],"mappings":"AAySA,wBAAsB,YAAY,CAChC,OAAO,EAAE,MAAM,EACf,IAAI,GAAE;IAAE,MAAM,CAAC,EAAE,MAAM,CAAC;IAAC,IAAI,CAAC,EAAE,OAAO,CAAC;IAAC,YAAY,CAAC,EAAE,MAAM,CAAA;CAAO,GACpE,OAAO,CAAC,IAAI,CAAC,CAYf"}
+{"version":3,"file":"watcher.d.ts","sourceRoot":"","sources":["../../../src/domain/graph/watcher.ts"],"names":[],"mappings":"AAoRA;;;;;;;;;;;GAWG;AACH,wBAAgB,4BAA4B,CAC1C,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,QAAQ,CAAC,MAAM,CAAC,GACxB,KAAK,CAAC;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,OAAO,CAAA;CAAE,CAAC,CAK3C;AAqBD,wBAAsB,YAAY,CAChC,OAAO,EAAE,MAAM,EACf,IAAI,GAAE;IAAE,MAAM,CAAC,EAAE,MAAM,CAAC;IAAC,IAAI,CAAC,EAAE,OAAO,CAAC;IAAC,YAAY,CAAC,EAAE,MAAM,CAAC;IAAC,MAAM,CAAC,EAAE,MAAM,CAAA;CAAO,GACrF,OAAO,CAAC,IAAI,CAAC,CAYf"}

package/dist/domain/graph/watcher.js

@@ -7,7 +7,7 @@ import { DbError } from '../../shared/errors.js';
 import { createParseTreeCache, getActiveEngine } from '../parser.js';
 import { rebuildFile } from './builder/incremental.js';
 import { appendChangeEvents, buildChangeEvent, diffSymbols } from './change-journal.js';
-import { appendJournalEntries } from './journal.js';
+import { appendJournalEntriesAndStampHeader } from './journal.js';
 function shouldIgnorePath(filePath) {
     const parts = filePath.split(path.sep);
     return parts.some((p) => shouldIgnore(p));
@@ -61,7 +61,7 @@ function writeJournalAndChangeEvents(rootDir, updates) {
         deleted: r.deleted || false,
     }));
     try {
-        appendJournalEntries(rootDir, entries);
+        appendJournalEntriesAndStampHeader(rootDir, entries, Date.now());
     }
     catch (e) {
         debug(`Journal write failed (non-fatal): ${e.message}`);
@@ -115,7 +115,7 @@ function collectTrackedFiles(dir, result) {
 }
 /** Initialize DB, engine, cache, and statements for watch mode. */
 function setupWatcher(rootDir, opts) {
-    const dbPath = path.join(rootDir, '.codegraph', 'graph.db');
+    const dbPath = opts.dbPath ?? path.join(rootDir, '.codegraph', 'graph.db');
     if (!fs.existsSync(dbPath)) {
         throw new DbError('No graph.db found. Run `codegraph build` first.', { file: dbPath });
     }
@@ -211,17 +211,33 @@ function startNativeWatcher(ctx) {
     });
     return () => watcher.close();
 }
+/**
+ * Build journal entries for a pending-path set, detecting deletions by
+ * existence check.
+ *
+ * `ctx.pending` is an untyped `Set<string>` — it carries no event-type
+ * metadata. Without this check, a file deleted during the watch session
+ * would be journaled as "changed", causing the next incremental build to
+ * try to re-parse a non-existent file instead of removing it from the graph.
+ * Mirrors the deletion detection in `rebuildFile` (see builder/incremental.ts).
+ *
+ * Exported for unit-testing; prefer `setupShutdownHandler` in production paths.
+ */
+export function buildFlushEntriesFromPending(rootDir, pending) {
+    return [...pending].map((filePath) => ({
+        file: normalizePath(path.relative(rootDir, filePath)),
+        deleted: !fs.existsSync(filePath),
+    }));
+}
 /** Register SIGINT handler to flush journal and clean up. */
 function setupShutdownHandler(ctx, cleanup) {
     process.once('SIGINT', () => {
         info('Stopping watcher...');
         cleanup();
         if (ctx.pending.size > 0) {
-            const entries = [...ctx.pending].map((filePath) => ({
-                file: normalizePath(path.relative(ctx.rootDir, filePath)),
-            }));
+            const entries = buildFlushEntriesFromPending(ctx.rootDir, ctx.pending);
             try {
-                appendJournalEntries(ctx.rootDir, entries);
+                appendJournalEntriesAndStampHeader(ctx.rootDir, entries, Date.now());
             }
             catch (e) {
                 debug(`Journal flush on exit failed (non-fatal): ${e.message}`);