@mmnto/totem 1.109.0 → 1.111.0

package/dist/ingest/pipeline.test.js

@@ -1,3 +1,4 @@
+import { execFileSync } from 'node:child_process';
 import * as fs from 'node:fs';
 import * as os from 'node:os';
 import * as path from 'node:path';
@@ -144,6 +145,461 @@ describe('runSync embedding guard', () => {
         await expect(runSync(config, { projectRoot: os.tmpdir(), incremental: false })).rejects.toThrow('No embedding provider configured');
     });
 });
+// ─── Full-sync crash recovery (#2562, ADR-115 Train-1 induced regression) ───
+//
+// The defect: `--full` reset the store, crashed mid-embed, and left the
+// previous SUCCESSFUL sync's baseline behind — so the next plain `totem sync`
+// diffed from the old SHA, saw 0 changed files, and reported "Sync complete:
+// 0 files" over the gutted store. These tests reproduce that state with a
+// crash-at-flush-K embedder and lock in the checkpoint/resume contract.
+const FULL_SYNC_CHECKPOINT_FILE = 'cache/full-sync-checkpoint.json';
+const HEAVY_TIMEOUT_MS = 60_000;
+/** Embeds deterministically; throws a quota-shaped 429 from call N onward. */
+class ScriptedEmbedder {
+    dimensions;
+    embedCalls = [];
+    failFromCall = null;
+    onCall;
+    /** Awaited at embed entry — lets a cell hold the embed open while timers fire (#2564). */
+    onCallAsync;
+    describeEffective;
+    resolveEffective;
+    calls = 0;
+    constructor(dimensions = 4) {
+        this.dimensions = dimensions;
+    }
+    async embed(texts) {
+        this.calls++;
+        this.onCall?.();
+        if (this.onCallAsync)
+            await this.onCallAsync();
+        if (this.failFromCall !== null && this.calls >= this.failFromCall) {
+            throw Object.assign(new Error('quota exceeded: RESOURCE_EXHAUSTED'), { status: 429 });
+        }
+        this.embedCalls.push([...texts]);
+        return texts.map((_, i) => new Array(this.dimensions).fill(i % 7));
+    }
+    /** All text embedded across every call, joined for content assertions. */
+    allText() {
+        return this.embedCalls.flat().join('\n');
+    }
+}
+describe('full-sync crash recovery (#2562)', () => {
+    let tmpDir;
+    let config;
+    const run = (embedder, incremental) => runSync(config, { projectRoot: tmpDir, incremental, embedder });
+    const checkpointPath = () => path.join(tmpDir, '.totem', FULL_SYNC_CHECKPOINT_FILE);
+    const syncStatePath = () => path.join(tmpDir, '.totem', 'cache/sync-state.json');
+    const git = (...args) => execFileSync('git', args, { cwd: tmpDir, stdio: 'pipe' });
+    /** Exactly 80 chunks per file (one per `##` section; the `#` preamble has
+     *  no body text, so it yields no chunk) — 240 total. Two files overflow
+     *  EMBED_BATCH_SIZE (100), so the first flush lands at a file boundary and
+     *  the crash-at-flush-2 embedder dies on the third file's flush with two
+     *  files already in the store. */
+    const TOTAL_CHUNKS = 240;
+    const writeCorpusFileTo = (dir, name, stem) => {
+        const sections = Array.from({ length: 80 }, (_, i) => `## ${stem} ${i}\n\n${stem}-content-${i}\n`).join('\n');
+        fs.writeFileSync(path.join(dir, name), `# ${stem}\n\n${sections}`, 'utf-8');
+    };
+    const writeCorpusFile = (name, stem) => writeCorpusFileTo(tmpDir, name, stem);
+    beforeEach(() => {
+        tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'totem-fullsync-'));
+        config = TotemConfigSchema.parse({
+            targets: [{ glob: '*.md', type: 'spec', strategy: 'markdown-heading' }],
+            embedding: { provider: 'gemini', model: 'test-model', dimensions: 4 },
+        });
+        writeCorpusFile('a.md', 'alpha');
+        writeCorpusFile('b.md', 'bravo');
+        writeCorpusFile('c.md', 'charlie');
+        git('init');
+        git('config', 'user.email', 'test@test.com');
+        git('config', 'user.name', 'Test');
+        git('add', '--', 'a.md', 'b.md', 'c.md');
+        git('commit', '-m', 'init');
+    });
+    afterEach(() => {
+        cleanTmpDir(tmpDir);
+    });
+    const ALL_FILES = ['a.md', 'b.md', 'c.md'];
+    const STEM = { 'a.md': 'alpha', 'b.md': 'bravo', 'c.md': 'charlie' };
+    const readCheckpoint = () => JSON.parse(fs.readFileSync(checkpointPath(), 'utf-8'));
+    /** The one file the crashed epoch never flushed (glob order is not guaranteed,
+     *  so which file that is must be READ from the checkpoint, not assumed). */
+    const unflushedFile = () => {
+        const { completedFiles } = readCheckpoint();
+        const missing = ALL_FILES.filter((f) => !completedFiles.includes(f));
+        expect(missing).toHaveLength(1);
+        return missing[0];
+    };
+    /** Crash a full sync at the second flush: two files land, the third does not. */
+    async function crashFullSync() {
+        const crasher = new ScriptedEmbedder();
+        crasher.failFromCall = 2;
+        await expect(run(crasher, false)).rejects.toThrow('RESOURCE_EXHAUSTED');
+        return crasher;
+    }
+    it('#2564: a lock stolen mid-embed aborts loudly at the flush boundary, keeps the marker, and leaves the thief lock intact', { timeout: HEAVY_TIMEOUT_MS }, async () => {
+        const lockFile = path.join(tmpDir, '.totem', 'sync.lock');
+        const foreign = {
+            pid: 424242,
+            timestamp: Date.now(),
+            createdAt: Date.now(),
+            holderId: 'thief-holder',
+        };
+        const embedder = new ScriptedEmbedder();
+        let swapped = false;
+        embedder.onCallAsync = async () => {
+            // First flush (two files) lands clean; the theft hits during the
+            // second flush's embed — the paced multi-minute window from the issue.
+            if (embedder.embedCalls.length >= 1 && !swapped) {
+                swapped = true;
+                fs.writeFileSync(lockFile, JSON.stringify(foreign));
+                // Idle long enough for a 25ms heartbeat to observe and latch.
+                await new Promise((r) => setTimeout(r, 300));
+            }
+        };
+        await expect(runSync(config, {
+            projectRoot: tmpDir,
+            incremental: false,
+            embedder,
+            lockOptions: { heartbeatIntervalMs: 25 },
+        })).rejects.toThrow('Sync lock was lost');
+        expect(swapped).toBe(true);
+        // The mutating degraded path preserved crash safety: the marker is
+        // intact...
+        expect(fs.existsSync(checkpointPath())).toBe(true);
+        // ...and the abort came from the flush EXIT probe, BEFORE the
+        // post-theft checkpoint append: only the two pre-theft files are
+        // checkpointed. Deleting the exit probe lets the last flush append the
+        // third file and fails here (leg MAJOR-1 — an existsSync check alone
+        // cannot tell WHICH probe fired). The ENTRY probe is not inducible
+        // in-process on the full path — no await exists between one flush's
+        // exit probe and the next flush's entry probe for a beat to latch in
+        // (leg MINOR-R1, disclosed); its marginal window is the incremental
+        // purge gap, and a miss converges at the next probe.
+        expect(readCheckpoint().completedFiles).toHaveLength(2);
+        // ...no completion-claiming baseline was written...
+        expect(fs.existsSync(syncStatePath())).toBe(false);
+        // ...and the thief's lock survived our release (no cascade theft).
+        expect(JSON.parse(fs.readFileSync(lockFile, 'utf-8'))).toEqual(foreign);
+        // Recovery control: with the thief gone, the next sync resumes the
+        // epoch and completes the full corpus — and actually re-embeds the
+        // un-checkpointed file (store.count() alone would pass on a zero-work
+        // resume, leg MAJOR-1).
+        fs.unlinkSync(lockFile);
+        const finisher = new ScriptedEmbedder();
+        const result = await run(finisher, false);
+        expect(result.totalChunks).toBe(TOTAL_CHUNKS);
+        expect(finisher.embedCalls.length).toBeGreaterThan(0);
+        expect(fs.existsSync(checkpointPath())).toBe(false);
+    });
+    it('a crashed --full leaves the dirty marker with only fully-flushed files checkpointed', { timeout: HEAVY_TIMEOUT_MS }, async () => {
+        const crasher = new ScriptedEmbedder();
+        crasher.failFromCall = 2;
+        let markerSeenDuringEmbed = false;
+        crasher.onCall = () => {
+            markerSeenDuringEmbed ||= fs.existsSync(checkpointPath());
+        };
+        await expect(run(crasher, false)).rejects.toThrow('RESOURCE_EXHAUSTED');
+        // The marker was already on disk when the first embed call ran — no
+        // window exists where the store is reset but unmarked.
+        expect(markerSeenDuringEmbed).toBe(true);
+        // Exactly the two fully-flushed files are checkpointed; the file whose
+        // flush crashed is not (whole-file flush boundaries).
+        const cp = JSON.parse(fs.readFileSync(checkpointPath(), 'utf-8'));
+        expect(cp.completedFiles).toHaveLength(2);
+        expect(ALL_FILES.filter((f) => !cp.completedFiles.includes(f))).toHaveLength(1);
+        expect(cp.embedder).toEqual({ provider: 'gemini', model: 'test-model', dimensions: 4 });
+        expect(typeof cp.startedHeadSha).toBe('string');
+        // No successful sync ever completed — no baseline may exist.
+        expect(fs.existsSync(syncStatePath())).toBe(false);
+    });
+    it('INDUCED REGRESSION: the next plain sync resumes the full re-index instead of reporting complete over a partial store', { timeout: HEAVY_TIMEOUT_MS }, async () => {
+        // The lying sensor NEEDS a surviving baseline from a previous
+        // SUCCESSFUL sync: pre-fix, the crashed --full left this state file
+        // intact over the reset store, the next plain sync diffed
+        // lastSyncSha..HEAD, saw 0 changed files, and reported "Sync
+        // complete: 0 files" (falsification round 1, MAJOR 5 — without this
+        // baseline the pre-fix code fails via the git-diff fallback instead).
+        const first = await run(new ScriptedEmbedder(), false);
+        expect(first.totalChunks).toBe(TOTAL_CHUNKS);
+        const staleState = fs.readFileSync(syncStatePath(), 'utf-8');
+        await crashFullSync();
+        const missing = unflushedFile();
+        const flushed = ALL_FILES.filter((f) => f !== missing);
+        // The crash left the stale baseline byte-identical — the defect's
+        // exact precondition.
+        expect(fs.readFileSync(syncStatePath(), 'utf-8')).toBe(staleState);
+        const resumer = new ScriptedEmbedder();
+        const result = await run(resumer, true); // plain `totem sync`
+        // Pre-fix this reported 0 files processed over a partial store.
+        expect(result.filesProcessed).toBe(1);
+        expect(resumer.allText()).toContain(`${STEM[missing]}-content-1`);
+        for (const kept of flushed) {
+            expect(resumer.allText()).not.toContain(`${STEM[kept]}-content-1`);
+        }
+        // The store now holds the whole corpus, the marker is gone, and the
+        // baseline points at HEAD — the epoch completed for real.
+        expect(result.totalChunks).toBe(TOTAL_CHUNKS);
+        expect(fs.existsSync(checkpointPath())).toBe(false);
+        const state = JSON.parse(fs.readFileSync(syncStatePath(), 'utf-8'));
+        const headSha = execFileSync('git', ['rev-parse', 'HEAD'], {
+            cwd: tmpDir,
+            encoding: 'utf-8',
+        }).trim();
+        expect(state.lastSyncSha).toBe(headSha);
+    });
+    it('a file changed since the crashed epoch re-embeds on resume', { timeout: HEAVY_TIMEOUT_MS }, async () => {
+        await crashFullSync();
+        const missing = unflushedFile();
+        const [mutated, untouched] = ALL_FILES.filter((f) => f !== missing);
+        fs.appendFileSync(path.join(tmpDir, mutated), `\n## ${STEM[mutated]} extra\n\n${STEM[mutated]}-mutated\n`, 'utf-8');
+        git('add', '--', mutated);
+        git('commit', '-m', 'mutate a flushed file');
+        const resumer = new ScriptedEmbedder();
+        const result = await run(resumer, true);
+        // The changed-since-epoch flushed file re-embeds alongside the
+        // never-flushed one; the untouched flushed file stays skipped.
+        expect(result.filesProcessed).toBe(2);
+        expect(resumer.allText()).toContain(`${STEM[mutated]}-mutated`);
+        expect(resumer.allText()).toContain(`${STEM[missing]}-content-1`);
+        expect(resumer.allText()).not.toContain(`${STEM[untouched]}-content-1`);
+    });
+    it('GT round: a completed file EMPTIED since the epoch purges its stale rows on resume', { timeout: HEAVY_TIMEOUT_MS }, async () => {
+        await crashFullSync();
+        const missing = unflushedFile();
+        const [emptied] = ALL_FILES.filter((f) => f !== missing);
+        // The file now yields ZERO chunks. Its old rows must still purge —
+        // after this run the baseline advances past the change, so no later
+        // incremental diff revisits it and stale rows would be searchable
+        // forever (#2569 Greptile P1).
+        fs.writeFileSync(path.join(tmpDir, emptied), `# ${STEM[emptied]}\n`, 'utf-8');
+        git('add', '--', emptied);
+        git('commit', '-m', 'empty a flushed file');
+        const resumer = new ScriptedEmbedder();
+        const result = await run(resumer, true);
+        // The emptied file's 80 rows are gone; the never-flushed file's 80 landed.
+        expect(result.totalChunks).toBe(TOTAL_CHUNKS - 80);
+        expect(resumer.allText()).not.toContain(`${STEM[emptied]}-content-1`);
+        expect(fs.existsSync(checkpointPath())).toBe(false);
+    });
+    it('a corrupt checkpoint is dirty-but-unusable: the full re-index restarts from zero', { timeout: HEAVY_TIMEOUT_MS }, async () => {
+        await crashFullSync();
+        fs.writeFileSync(checkpointPath(), '{ not json !!', 'utf-8');
+        const resumer = new ScriptedEmbedder();
+        const result = await run(resumer, true);
+        expect(result.filesProcessed).toBe(3);
+        expect(fs.existsSync(checkpointPath())).toBe(false);
+    });
+    it('an embedder-config change makes checkpointed progress unusable — restart from zero', { timeout: HEAVY_TIMEOUT_MS }, async () => {
+        await crashFullSync();
+        const differentDims = new ScriptedEmbedder(8);
+        const result = await run(differentDims, true);
+        expect(result.filesProcessed).toBe(3);
+        expect(differentDims.allText()).toContain('alpha-content-1');
+        expect(fs.existsSync(checkpointPath())).toBe(false);
+    });
+    it('a marker-write failure aborts BEFORE the store is destroyed', { timeout: HEAVY_TIMEOUT_MS }, async () => {
+        const healthy = new ScriptedEmbedder();
+        const first = await run(healthy, false);
+        expect(first.totalChunks).toBe(TOTAL_CHUNKS);
+        // Occupy the checkpoint path with a directory. The run first reads it
+        // as a checkpoint (EISDIR → dirty-but-unusable), then the restart's
+        // marker write fails at the atomic rename — and the reset never runs.
+        fs.mkdirSync(checkpointPath(), { recursive: true });
+        await expect(run(new ScriptedEmbedder(), false)).rejects.toThrow();
+        fs.rmSync(checkpointPath(), { recursive: true, force: true });
+        fs.rmSync(`${checkpointPath()}.${process.pid}.tmp`, { force: true });
+        // The store survived the aborted run: a plain incremental sync sees a
+        // clean baseline and the full chunk count, not an empty or partial store.
+        const after = await run(new ScriptedEmbedder(), true);
+        expect(after.filesProcessed).toBe(0);
+        expect(after.totalChunks).toBe(first.totalChunks);
+    });
+    // ─── Falsification round 1 regressions ───
+    it('MAJOR 1: a store emptied under a live checkpoint is re-embedded in full, not trusted from paper', { timeout: HEAVY_TIMEOUT_MS }, async () => {
+        const first = await run(new ScriptedEmbedder(), false);
+        expect(first.totalChunks).toBe(TOTAL_CHUNKS);
+        await crashFullSync();
+        // Simulate the heal-by-nuke path (LanceStore.connect on a corrupt
+        // dataset): the store vanishes while the checkpoint still claims two
+        // files are embedded.
+        fs.rmSync(path.join(tmpDir, config.lanceDir), { recursive: true, force: true });
+        const resumer = new ScriptedEmbedder();
+        const result = await run(resumer, true);
+        // Pre-fold this embedded ONLY the unflushed file over an empty store
+        // and wrote a clean baseline — the #2562 lying sensor by another door.
+        expect(result.filesProcessed).toBe(3);
+        expect(result.totalChunks).toBe(TOTAL_CHUNKS);
+        expect(fs.existsSync(checkpointPath())).toBe(false);
+    });
+    it('MAJOR 2: untracked corpus files stay checkpointed across a resume (quota convergence)', { timeout: HEAVY_TIMEOUT_MS }, async () => {
+        // Make the corpus untracked-but-live: git has no history for it, so it
+        // is a PERMANENT member of git's changed-union. Pre-fold that union
+        // evicted these files from the completed set on every resume — quota
+        // re-spent on the same files forever, never converging.
+        git('rm', '--cached', '--', 'a.md', 'b.md', 'c.md');
+        git('commit', '-m', 'untrack corpus');
+        await crashFullSync();
+        const missing = unflushedFile();
+        const resumer = new ScriptedEmbedder();
+        const result = await run(resumer, true);
+        expect(result.filesProcessed).toBe(1);
+        expect(resumer.allText()).toContain(`${STEM[missing]}-content-1`);
+        expect(result.totalChunks).toBe(TOTAL_CHUNKS);
+        expect(fs.existsSync(checkpointPath())).toBe(false);
+    });
+    it('MAJOR 2: an untracked completed file MODIFIED after the crash still re-embeds (mtime arm)', { timeout: HEAVY_TIMEOUT_MS }, async () => {
+        git('rm', '--cached', '--', 'a.md', 'b.md', 'c.md');
+        git('commit', '-m', 'untrack corpus');
+        await crashFullSync();
+        const missing = unflushedFile();
+        const [mutated] = ALL_FILES.filter((f) => f !== missing);
+        // Ensure the edit's mtime lands measurably after the epoch start.
+        await new Promise((resolve) => setTimeout(resolve, 20));
+        fs.appendFileSync(path.join(tmpDir, mutated), `\n## ${STEM[mutated]} extra\n\n${STEM[mutated]}-mutated\n`, 'utf-8');
+        const resumer = new ScriptedEmbedder();
+        const result = await run(resumer, true);
+        expect(result.filesProcessed).toBe(2); // mutated (mtime > epoch) + never-flushed
+        expect(resumer.allText()).toContain(`${STEM[mutated]}-mutated`);
+        expect(resumer.allText()).toContain(`${STEM[missing]}-content-1`);
+    });
+    it('MAJOR 3: a checkpoint stamped with a fallback embedder identity restarts instead of resuming', { timeout: HEAVY_TIMEOUT_MS }, async () => {
+        // The crashing run's embedder reports an EFFECTIVE identity (the
+        // LazyEmbedder Ollama-fallback shape) that differs from the configured
+        // gemini fingerprint — the checkpoint must record the effective one.
+        const crasher = new ScriptedEmbedder();
+        crasher.failFromCall = 2;
+        crasher.describeEffective = () => ({
+            provider: 'ollama',
+            model: 'nomic-embed-text',
+            dimensions: 4,
+        });
+        await expect(run(crasher, false)).rejects.toThrow('RESOURCE_EXHAUSTED');
+        const cp = JSON.parse(fs.readFileSync(checkpointPath(), 'utf-8'));
+        expect(cp.embedder.provider).toBe('ollama');
+        // The resume runs under the configured gemini fingerprint — the
+        // stamped ollama progress is unusable: vector spaces must not mix.
+        const resumer = new ScriptedEmbedder();
+        const result = await run(resumer, true);
+        expect(result.filesProcessed).toBe(3);
+        expect(result.totalChunks).toBe(TOTAL_CHUNKS);
+    });
+    it('F2: a PERSISTENT fallback resumes as itself instead of restart-looping', { timeout: HEAVY_TIMEOUT_MS }, async () => {
+        const ollamaId = { provider: 'ollama', model: 'nomic-embed-text', dimensions: 4 };
+        const crasher = new ScriptedEmbedder();
+        crasher.failFromCall = 2;
+        crasher.describeEffective = () => ollamaId;
+        await expect(run(crasher, false)).rejects.toThrow('RESOURCE_EXHAUSTED');
+        const missing = unflushedFile();
+        // The fallback persists into the next run: it resolves to the SAME
+        // effective identity, so the epoch continues. Pre-fold, the gate
+        // compared the stamped ollama identity against the CONFIG (gemini)
+        // fingerprint and restart-looped forever, resetting the store on
+        // every attempt — a corpus needing more than one run never completed.
+        const resumer = new ScriptedEmbedder();
+        resumer.resolveEffective = () => Promise.resolve(ollamaId);
+        const result = await run(resumer, true);
+        expect(result.filesProcessed).toBe(1);
+        expect(resumer.allText()).toContain(`${STEM[missing]}-content-1`);
+        expect(result.totalChunks).toBe(TOTAL_CHUNKS);
+        expect(fs.existsSync(checkpointPath())).toBe(false);
+    });
+    it('F1: a run falling back mid-resume restarts BEFORE inserting into the genuine epoch', { timeout: HEAVY_TIMEOUT_MS }, async () => {
+        await crashFullSync(); // checkpoint carries the genuine (gemini) fingerprint
+        // This run's embedder RESOLVES to an ollama fallback. The gate must
+        // compare effective-vs-effective and restart — pre-fold it compared
+        // config-vs-stamped (gemini vs gemini → match) and ollama vectors were
+        // inserted beside the epoch's gemini rows, mixing vector spaces.
+        const resumer = new ScriptedEmbedder();
+        resumer.resolveEffective = () => Promise.resolve({ provider: 'ollama', model: 'nomic-embed-text', dimensions: 4 });
+        const result = await run(resumer, true);
+        expect(result.filesProcessed).toBe(3);
+        expect(result.totalChunks).toBe(TOTAL_CHUNKS);
+        expect(fs.existsSync(checkpointPath())).toBe(false);
+    });
+    it('MINOR 10: a zero-work resume clears the marker WITHOUT requiring an embedder', { timeout: HEAVY_TIMEOUT_MS }, async () => {
+        // Epoch crashed between its final flush and the marker delete: the
+        // store is complete but the marker survives. The resume has nothing to
+        // embed, so the identity gate must not force embedder resolution — a
+        // missing embedder would otherwise wedge the epoch closed forever.
+        const first = await run(new ScriptedEmbedder(), false);
+        expect(first.totalChunks).toBe(TOTAL_CHUNKS);
+        const headSha = execFileSync('git', ['rev-parse', 'HEAD'], {
+            cwd: tmpDir,
+            encoding: 'utf-8',
+        }).trim();
+        fs.writeFileSync(checkpointPath(), JSON.stringify({
+            startedHeadSha: headSha,
+            startedAt: Date.now(),
+            indexExclusionHash: 'whatever',
+            embedder: { provider: 'gemini', model: 'test-model', dimensions: 4 },
+            completedFiles: ALL_FILES,
+        }), 'utf-8');
+        const unresolvable = new ScriptedEmbedder();
+        unresolvable.resolveEffective = () => Promise.reject(new Error('no embedder available'));
+        const result = await run(unresolvable, true);
+        expect(result.filesProcessed).toBe(0);
+        expect(unresolvable.embedCalls).toHaveLength(0);
+        expect(result.totalChunks).toBe(TOTAL_CHUNKS);
+        expect(fs.existsSync(checkpointPath())).toBe(false);
+    });
+    it('ROUND 4: a RESOLVABLE identity mismatch restarts even with zero work remaining', { timeout: HEAVY_TIMEOUT_MS }, async () => {
+        // The zero-work exemption is for RESOLUTION FAILURE only. A resolvable
+        // mismatch with nothing left to embed must still restart: clearing the
+        // marker would rewrite index-meta to the new identity and launder the
+        // DATABASE_MISMATCH evidence over a store built in the old space.
+        const first = await run(new ScriptedEmbedder(), false);
+        expect(first.totalChunks).toBe(TOTAL_CHUNKS);
+        const headSha = execFileSync('git', ['rev-parse', 'HEAD'], {
+            cwd: tmpDir,
+            encoding: 'utf-8',
+        }).trim();
+        fs.writeFileSync(checkpointPath(), JSON.stringify({
+            startedHeadSha: headSha,
+            startedAt: Date.now(),
+            indexExclusionHash: 'whatever',
+            embedder: { provider: 'ollama', model: 'nomic-embed-text', dimensions: 4 },
+            completedFiles: ALL_FILES,
+        }), 'utf-8');
+        // Plain resolvable embedder — falls back to the config (gemini)
+        // fingerprint, which mismatches the stamped ollama identity.
+        const resumer = new ScriptedEmbedder();
+        const result = await run(resumer, true);
+        expect(result.filesProcessed).toBe(3); // restarted, not cleared
+        expect(result.totalChunks).toBe(TOTAL_CHUNKS);
+        expect(fs.existsSync(checkpointPath())).toBe(false);
+    });
+    it('MAJOR 4: a non-git project resumes via the mtime arm instead of restarting every run', { timeout: HEAVY_TIMEOUT_MS }, async () => {
+        const dir = fs.mkdtempSync(path.join(os.tmpdir(), 'totem-nongit-'));
+        try {
+            writeCorpusFileTo(dir, 'a.md', 'alpha');
+            writeCorpusFileTo(dir, 'b.md', 'bravo');
+            writeCorpusFileTo(dir, 'c.md', 'charlie');
+            const crasher = new ScriptedEmbedder();
+            crasher.failFromCall = 2;
+            await expect(runSync(config, { projectRoot: dir, incremental: false, embedder: crasher })).rejects.toThrow('RESOURCE_EXHAUSTED');
+            const cpPath = path.join(dir, '.totem', FULL_SYNC_CHECKPOINT_FILE);
+            const cp = JSON.parse(fs.readFileSync(cpPath, 'utf-8'));
+            expect(cp.startedHeadSha).toBeNull();
+            expect(cp.completedFiles).toHaveLength(2);
+            const resumer = new ScriptedEmbedder();
+            const result = await runSync(config, {
+                projectRoot: dir,
+                incremental: true,
+                embedder: resumer,
+            });
+            // Pre-fold, null startedHeadSha mapped to restart-from-zero on every
+            // run — the population with no diff signal could never converge.
+            expect(result.filesProcessed).toBe(1);
+            expect(result.totalChunks).toBe(TOTAL_CHUNKS);
+            expect(fs.existsSync(cpPath)).toBe(false);
+        }
+        finally {
+            cleanTmpDir(dir);
+        }
+    });
+});
 describe('buildIndexManifest', () => {
     const writtenAt = new Date('2026-05-07T00:00:00.000Z');
     const docs = [

package/dist/ingest/pipeline.test.js.map

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package/dist/ingest/sync.d.ts

@@ -1,5 +1,5 @@
 export type { ResolvedFile } from './file-resolver.js';
-export { getChangedFiles, getHeadSha, resolveFiles } from './file-resolver.js';
+export { getChangedFiles, getChangedFilesDetailed, getHeadSha, resolveFiles, } from './file-resolver.js';
 export type { IndexManifest, ManifestDocument } from './pipeline.js';
-export { buildIndexManifest, INDEX_MANIFEST_SCHEMA, runSync, verifyIndexMeta } from './pipeline.js';
+export { buildIndexManifest, hasFullSyncCheckpoint, INDEX_MANIFEST_SCHEMA, runSync, verifyIndexMeta, } from './pipeline.js';
 //# sourceMappingURL=sync.d.ts.map

package/dist/ingest/sync.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"sync.d.ts","sourceRoot":"","sources":["../../src/ingest/sync.ts"],"names":[],"mappings":"AAAA,YAAY,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AACvD,OAAO,EAAE,eAAe,EAAE,UAAU,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AAC/E,YAAY,EAAE,aAAa,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AACrE,OAAO,EAAE,kBAAkB,EAAE,qBAAqB,EAAE,OAAO,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC"}
+{"version":3,"file":"sync.d.ts","sourceRoot":"","sources":["../../src/ingest/sync.ts"],"names":[],"mappings":"AAAA,YAAY,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AACvD,OAAO,EACL,eAAe,EACf,uBAAuB,EACvB,UAAU,EACV,YAAY,GACb,MAAM,oBAAoB,CAAC;AAC5B,YAAY,EAAE,aAAa,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AACrE,OAAO,EACL,kBAAkB,EAClB,qBAAqB,EACrB,qBAAqB,EACrB,OAAO,EACP,eAAe,GAChB,MAAM,eAAe,CAAC"}

package/dist/ingest/sync.js

@@ -1,3 +1,3 @@
-export { getChangedFiles, getHeadSha, resolveFiles } from './file-resolver.js';
-export { buildIndexManifest, INDEX_MANIFEST_SCHEMA, runSync, verifyIndexMeta } from './pipeline.js';
+export { getChangedFiles, getChangedFilesDetailed, getHeadSha, resolveFiles, } from './file-resolver.js';
+export { buildIndexManifest, hasFullSyncCheckpoint, INDEX_MANIFEST_SCHEMA, runSync, verifyIndexMeta, } from './pipeline.js';
 //# sourceMappingURL=sync.js.map

package/dist/ingest/sync.js.map

@@ -1 +1 @@
-{"version":3,"file":"sync.js","sourceRoot":"","sources":["../../src/ingest/sync.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,eAAe,EAAE,UAAU,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AAE/E,OAAO,EAAE,kBAAkB,EAAE,qBAAqB,EAAE,OAAO,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC"}
+{"version":3,"file":"sync.js","sourceRoot":"","sources":["../../src/ingest/sync.ts"],"names":[],"mappings":"AACA,OAAO,EACL,eAAe,EACf,uBAAuB,EACvB,UAAU,EACV,YAAY,GACb,MAAM,oBAAoB,CAAC;AAE5B,OAAO,EACL,kBAAkB,EAClB,qBAAqB,EACrB,qBAAqB,EACrB,OAAO,EACP,eAAe,GAChB,MAAM,eAAe,CAAC"}

package/dist/ledger.d.ts

@@ -164,9 +164,9 @@ export declare const LedgerEventSchema: z.ZodEffects<z.ZodObject<{
     qbd_correlation_id: z.ZodOptional<z.ZodString>;
 }, "strip", z.ZodTypeAny, {
     type: "suppress" | "corpus_query" | "derive_action" | "override" | "exemption" | "mcp_call" | "tool_call_first_significant" | "hook_fire" | "session_start" | "compile_run" | "claim_discipline_finding" | "compile_cache_decision";
+    timestamp: string;
     justification: string;
     source: "lint" | "shield" | "bot";
-    timestamp: string;
     immutable?: boolean | undefined;
     file?: string | undefined;
     line?: number | undefined;
@@ -180,8 +180,8 @@ export declare const LedgerEventSchema: z.ZodEffects<z.ZodObject<{
     qbd_correlation_id?: string | undefined;
 }, {
     type: "suppress" | "corpus_query" | "derive_action" | "override" | "exemption" | "mcp_call" | "tool_call_first_significant" | "hook_fire" | "session_start" | "compile_run" | "claim_discipline_finding" | "compile_cache_decision";
-    source: "lint" | "shield" | "bot";
     timestamp: string;
+    source: "lint" | "shield" | "bot";
     immutable?: boolean | undefined;
     file?: string | undefined;
     line?: number | undefined;
@@ -196,9 +196,9 @@ export declare const LedgerEventSchema: z.ZodEffects<z.ZodObject<{
     qbd_correlation_id?: string | undefined;
 }>, {
     type: "suppress" | "corpus_query" | "derive_action" | "override" | "exemption" | "mcp_call" | "tool_call_first_significant" | "hook_fire" | "session_start" | "compile_run" | "claim_discipline_finding" | "compile_cache_decision";
+    timestamp: string;
     justification: string;
     source: "lint" | "shield" | "bot";
-    timestamp: string;
     immutable?: boolean | undefined;
     file?: string | undefined;
     line?: number | undefined;
@@ -212,8 +212,8 @@ export declare const LedgerEventSchema: z.ZodEffects<z.ZodObject<{
     qbd_correlation_id?: string | undefined;
 }, {
     type: "suppress" | "corpus_query" | "derive_action" | "override" | "exemption" | "mcp_call" | "tool_call_first_significant" | "hook_fire" | "session_start" | "compile_run" | "claim_discipline_finding" | "compile_cache_decision";
-    source: "lint" | "shield" | "bot";
     timestamp: string;
+    source: "lint" | "shield" | "bot";
     immutable?: boolean | undefined;
     file?: string | undefined;
     line?: number | undefined;