@mmnto/totem 1.108.0 → 1.110.0

package/dist/ingest/pipeline.d.ts

@@ -11,6 +11,15 @@ import type { SyncOptions } from '../types.js';
  * Throws TotemDatabaseError if the provider has changed.
  */
 export declare function verifyIndexMeta(totemDir: string, config: TotemConfig): void;
+/**
+ * Whether a full re-index epoch is in progress (its dirty marker exists) for
+ * the given totem dir (#2562). Exposed for callers that spawn or gate syncs
+ * under bounded budgets — e.g. the MCP add-lesson tool's 60s-killed
+ * convenience sync, which a promoted paced resume can never finish
+ * (falsification round 3, MAJOR 1): such callers should skip and defer to the
+ * running epoch instead of timing out against it.
+ */
+export declare function hasFullSyncCheckpoint(totemDir: string): boolean;
 /**
  * One entry in the index-manifest `documents[]` array.
  *

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

@@ -1 +1 @@
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+{"version":3,"file":"pipeline.d.ts","sourceRoot":"","sources":["../../src/ingest/pipeline.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AAQvD,OAAO,KAAK,EAA6B,WAAW,EAAa,MAAM,aAAa,CAAC;AA+CrF;;;GAGG;AACH;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,GAAG,IAAI,CAuB3E;AAuFD;;;;;;;GAOG;AACH,wBAAgB,qBAAqB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAE/D;AAkBD;;;;;;;;GAQG;AACH,MAAM,WAAW,gBAAgB;IAC/B,UAAU,EAAE,MAAM,CAAC;IACnB;;;;OAIG;IACH,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,MAAM,CAAC;IACjB,+FAA+F;IAC/F,UAAU,EAAE,MAAM,CAAC;CACpB;AAED;;;;;;;;;;;GAWG;AACH,MAAM,WAAW,aAAa;IAC5B,MAAM,EAAE,MAAM,CAAC;IACf,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,gBAAgB,EAAE,CAAC;IAC9B,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,2EAA2E;AAC3E,eAAO,MAAM,qBAAqB,8BAA8B,CAAC;AAEjE;;;;;;;;;;;;GAYG;AACH,wBAAgB,kBAAkB,CAAC,KAAK,EAAE;IACxC,SAAS,EAAE,gBAAgB,EAAE,CAAC;IAC9B,OAAO,EAAE,MAAM,GAAG,IAAI,GAAG,SAAS,CAAC;IACnC,SAAS,EAAE,IAAI,CAAC;CACjB,GAAG,aAAa,CAUhB;AAED,wBAAsB,OAAO,CAC3B,MAAM,EAAE,WAAW,EACnB,OAAO,EAAE,WAAW,GACnB,OAAO,CAAC;IACT,eAAe,EAAE,MAAM,CAAC;IACxB,cAAc,EAAE,MAAM,CAAC;IACvB,WAAW,EAAE,MAAM,CAAC;IACpB,aAAa,EAAE,MAAM,CAAC;CACvB,CAAC,CAUD;AAYD;;;;;;;GAOG;AACH,wBAAgB,kBAAkB,CAChC,eAAe,EAAE,MAAM,EAAE,EACzB,iBAAiB,EAAE,MAAM,EAAE,GAC1B,MAAM,EAAE,CAGV;AAED;;;;;;;;GAQG;AACH,wBAAgB,qBAAqB,CAAC,QAAQ,EAAE,MAAM,EAAE,GAAG,MAAM,CAIhE;AAED;;;;;;;;GAQG;AACH,wBAAgB,yBAAyB,CACvC,iBAAiB,EAAE,MAAM,EAAE,EAC3B,eAAe,EAAE,MAAM,EAAE,GACxB,MAAM,EAAE,CAGV"}

package/dist/ingest/pipeline.js

@@ -9,10 +9,11 @@ import { withLock } from '../lock.js';
 import { sanitizeForIngestion } from '../sanitize.js';
 import { LanceStore } from '../store/lance-store.js';
 import { sanitizeForTerminal } from '../terminal-sanitize.js';
-import { getChangedFiles, getHeadSha, resolveFiles } from './file-resolver.js';
+import { getChangedFiles, getChangedFilesDetailed, getHeadSha, resolveFiles, } from './file-resolver.js';
 const EMBED_BATCH_SIZE = 100;
 const SYNC_STATE_FILE = 'cache/sync-state.json';
 const INDEX_META_FILE = 'cache/index-meta.json';
+const FULL_SYNC_CHECKPOINT_FILE = 'cache/full-sync-checkpoint.json';
 function readIndexMeta(totemDir) {
     const metaPath = path.join(totemDir, INDEX_META_FILE);
     try {
@@ -83,11 +84,79 @@ function readSyncState(totemDir, onProgress) {
         return null;
     }
 }
+/**
+ * Atomic JSON write (tmp + rename): a crash mid-write must never leave a torn
+ * state file — sync state and the full-sync checkpoint are both trusted by the
+ * NEXT run's control flow (#2562), matching the index-manifest write pattern.
+ */
+function writeJsonAtomic(filePath, value) {
+    fs.mkdirSync(path.dirname(filePath), { recursive: true });
+    // PID-unique tmp name: two writers racing under a stolen stale lock must
+    // not interleave through one tmp path (falsification round 1, MINOR 6).
+    const tmpPath = `${filePath}.${process.pid}.tmp`;
+    fs.writeFileSync(tmpPath, JSON.stringify(value, null, 2) + '\n', 'utf-8');
+    fs.renameSync(tmpPath, filePath);
+}
 function writeSyncState(totemDir, state) {
-    const statePath = path.join(totemDir, SYNC_STATE_FILE);
-    const dir = path.dirname(statePath);
-    fs.mkdirSync(dir, { recursive: true });
-    fs.writeFileSync(statePath, JSON.stringify(state, null, 2) + '\n', 'utf-8');
+    writeJsonAtomic(path.join(totemDir, SYNC_STATE_FILE), state);
+}
+/**
+ * Read the full-sync checkpoint (#2562). The caller has already established
+ * the file EXISTS (existence = the dirty marker); a parse/shape failure here
+ * means "dirty but unusable" — the caller restarts the full re-index from
+ * zero. A present-but-corrupt checkpoint is never treated as a clean state.
+ */
+function readFullSyncCheckpoint(totemDir, onProgress) {
+    const cpPath = path.join(totemDir, FULL_SYNC_CHECKPOINT_FILE);
+    try {
+        const parsed = JSON.parse(fs.readFileSync(cpPath, 'utf-8'));
+        if (parsed &&
+            (parsed.startedHeadSha === null || typeof parsed.startedHeadSha === 'string') &&
+            typeof parsed.startedAt === 'number' &&
+            typeof parsed.indexExclusionHash === 'string' &&
+            typeof parsed.embedder?.provider === 'string' &&
+            typeof parsed.embedder?.model === 'string' &&
+            typeof parsed.embedder?.dimensions === 'number' &&
+            Array.isArray(parsed.completedFiles) &&
+            parsed.completedFiles.every((f) => typeof f === 'string')) {
+            return parsed;
+        }
+        onProgress?.(`Warning: malformed full-sync checkpoint at ${cpPath} — ignoring its progress.`);
+        return null;
+        // totem-context: intentional warn+null on an unreadable checkpoint (mmnto-ai/totem#2562) — dirty-but-unusable restarts the full re-index from zero; failing the sync over a torn checkpoint would wedge every subsequent run.
+    }
+    catch (err) {
+        onProgress?.(`Warning: failed to read full-sync checkpoint: ${err instanceof Error ? err.message : String(err)}`);
+        return null;
+    }
+}
+function writeFullSyncCheckpoint(totemDir, checkpoint) {
+    writeJsonAtomic(path.join(totemDir, FULL_SYNC_CHECKPOINT_FILE), checkpoint);
+}
+/**
+ * Whether a full re-index epoch is in progress (its dirty marker exists) for
+ * the given totem dir (#2562). Exposed for callers that spawn or gate syncs
+ * under bounded budgets — e.g. the MCP add-lesson tool's 60s-killed
+ * convenience sync, which a promoted paced resume can never finish
+ * (falsification round 3, MAJOR 1): such callers should skip and defer to the
+ * running epoch instead of timing out against it.
+ */
+export function hasFullSyncCheckpoint(totemDir) {
+    return fs.existsSync(path.join(totemDir, FULL_SYNC_CHECKPOINT_FILE));
+}
+/**
+ * Best-effort marker delete at successful completion. A failed delete is loud
+ * but non-fatal: the next run resumes-full as a near-noop and retries the
+ * delete, so correctness converges (#2562).
+ */
+function deleteFullSyncCheckpoint(totemDir, onProgress) {
+    try {
+        fs.rmSync(path.join(totemDir, FULL_SYNC_CHECKPOINT_FILE), { force: true });
+        // totem-context: intentional best-effort delete (mmnto-ai/totem#2562) — a failed marker delete only makes the next run resume-full as a near-noop and retry it; aborting a fully-successful sync over it would be the drift.
+    }
+    catch (err) {
+        onProgress?.(`Warning: failed to delete full-sync checkpoint: ${err instanceof Error ? err.message : String(err)}`);
+    }
 }
 /** Current schema identifier persisted to `.totem/index-manifest.json`. */
 export const INDEX_MANIFEST_SCHEMA = 'totem-index-manifest-v0.2';
@@ -175,15 +244,38 @@ async function runSyncInner(config, options) {
     const log = onProgress ?? (() => { });
     // 0. Capture HEAD SHA early — before any async work that might race with new commits
     const headSha = getHeadSha(projectRoot, log);
-    // 1. Create embedder
+    // 1. Create embedder (or take the injected one — tests / embedding hosts).
+    // `log` is threaded through so a LazyEmbedder Ollama fallback is AUDIBLE —
+    // a silent vector-space switch mid-sync is sensor degradation (#2562).
     const embedding = requireEmbedding(config);
     log('Initializing embedding provider...');
-    const embedder = createEmbedder(embedding);
+    const embedder = options.embedder ?? createEmbedder(embedding, log);
+    // Resume-compatibility fingerprint (#2562): a checkpointed epoch may only
+    // continue under the embedder configuration that started it — vectors from
+    // two configurations must never mix in one store. Mirrors writeIndexMeta.
+    const embedderFingerprint = {
+        provider: embedding.provider,
+        model: embedding.model ?? 'default',
+        dimensions: embedder.dimensions,
+    };
     // 2. Connect to store
     const storePath = path.join(projectRoot, config.lanceDir);
     const store = new LanceStore(storePath, embedder, { absolutePathRoot: projectRoot });
     await store.connect();
-    // 2b. Auto-heal: force full sync when incremental is requested but DB is empty
+    const totemDir = path.join(projectRoot, config.totemDir);
+    // 2b (#2562). A live checkpoint marks an unfinished full re-index. It takes
+    // precedence over the requested mode — the partial store must complete
+    // before any incremental diff can be trusted again — and it subsumes the
+    // empty-store heal below (an interrupted full that never flushed).
+    let resumeFrom = null;
+    if (hasFullSyncCheckpoint(totemDir)) {
+        incremental = false;
+        resumeFrom = readFullSyncCheckpoint(totemDir, log);
+        log(resumeFrom
+            ? `Previous full re-index did not complete — resuming it (${resumeFrom.completedFiles.length} file(s) checkpointed).`
+            : 'Previous full re-index did not complete — restarting it from zero.');
+    }
+    // 2c. Auto-heal: force full sync when incremental is requested but DB is empty
     if (incremental && (await store.isEmpty())) {
         log('Empty database detected. Forcing full sync...');
         incremental = false;
@@ -191,7 +283,6 @@ async function runSyncInner(config, options) {
     // 3. Resolve files to process. Index exclusion unions both keys:
     // `ignorePatterns` (legacy dual-scope) + `indexIgnorePatterns` (index-only,
     // mmnto-ai/totem#1748) — only the former also gates lint/shield scope.
-    const totemDir = path.join(projectRoot, config.totemDir);
     const exclusionPatterns = [...config.ignorePatterns, ...config.indexIgnorePatterns];
     const allFiles = resolveFiles(config.targets, projectRoot, exclusionPatterns, log);
     // Order-normalized hash of the effective exclusion set — persisted below and
@@ -199,6 +290,26 @@ async function runSyncInner(config, options) {
     const indexExclusionHash = hashIndexExclusionSet(exclusionPatterns);
     let filesToProcess;
     let deletedPaths = [];
+    // #2562: active-epoch checkpoint (full mode only) — written before the store
+    // is destroyed, appended after each successful flush, deleted on success.
+    let checkpoint = null;
+    let resumedWithoutReset = false;
+    const freshCheckpoint = () => ({
+        startedHeadSha: headSha,
+        startedAt: Date.now(),
+        indexExclusionHash,
+        embedder: embedderFingerprint,
+        completedFiles: [],
+    });
+    // The dirty marker MUST hit disk before the store is destroyed: a marker
+    // write failure aborts loudly with the store intact, so no window exists in
+    // which a reset store is unmarked (#2562).
+    async function beginFullSync(cp) {
+        writeFullSyncCheckpoint(totemDir, cp);
+        checkpoint = cp;
+        log('Full sync: resetting index...');
+        await store.reset();
+    }
     if (incremental) {
         // Persisted sync state carries both the diff baseline (lastSyncSha) and the
         // exclusion-set hash used for removal reconciliation (mmnto-ai/totem#2366).
@@ -212,7 +323,7 @@ async function runSyncInner(config, options) {
         const changedPaths = options.changedFiles ?? getChangedFiles(projectRoot, sinceRef, log);
         if (changedPaths === null) {
             log('Git diff failed, falling back to full sync...');
-            await store.reset();
+            await beginFullSync(freshCheckpoint());
             filesToProcess = allFiles;
             log(`Full sync (fallback): ${filesToProcess.length} files to process`);
         }
@@ -261,9 +372,126 @@ async function runSyncInner(config, options) {
                 ` (of ${allFiles.length} total)`);
         }
     }
+    else if (resumeFrom) {
+        // #2562 resume: NO reset — the interrupted epoch continues. Already-done
+        // derives from FOUR signals, not the checkpoint alone:
+        //   1. checkpointed (the epoch flushed it);
+        //   2. ∩ live (still resolved by the current target set);
+        //   3. ∩ actually-in-the-store — the store is ground truth: a store
+        //      healed/nuked under a live checkpoint must not be trusted from
+        //      paper (falsification round 1, MAJOR 1);
+        //   4. − moved-since-epoch: anything in git's tracked diff against
+        //      startedHeadSha, PLUS anything whose mtime postdates the epoch
+        //      start. The mtime arm applies to EVERY file, not only untracked
+        //      ones (falsification round 2, F3: submodule and assume-unchanged
+        //      files appear in neither git list, so an untracked-only mtime arm
+        //      silently kept them stale) — a false-positive eviction is just a
+        //      harmless re-embed. Untracked files are deliberately NOT evicted by
+        //      git-list membership (it is permanent — round 1, MAJOR 2), and a
+        //      non-git epoch (null startedHeadSha) has an empty tracked set, so
+        //      the mtime arm carries it alone (MAJOR 4).
+        // The epoch diff never derives from options.changedFiles — a caller's
+        // diff window says nothing about what the crashed epoch covered.
+        const detailed = resumeFrom.startedHeadSha
+            ? getChangedFilesDetailed(projectRoot, resumeFrom.startedHeadSha, log)
+            : { tracked: [], untracked: [] };
+        if (detailed === null) {
+            log('Cannot diff against the interrupted epoch — restarting the full re-index from zero.');
+            await beginFullSync(freshCheckpoint());
+            filesToProcess = allFiles;
+            log(`Full sync: ${filesToProcess.length} files to process`);
+        }
+        else {
+            let indexedRaw = null;
+            try {
+                indexedRaw = await store.getDistinctPaths();
+                // totem-context: intentional warn+degrade on a getDistinctPaths failure (mmnto-ai/totem#2562, falsification round 2 F7 + round 3 MINOR 9a) — the completed set collapses to EMPTY below (every file re-embeds via delete-first, same cost as a reset-restart) but the table is NOT destroyed over a possibly-transient read failure, and the checkpoint's paper progress is RETAINED untrusted so a second crash does not erase a prior epoch's flushed work.
+            }
+            catch (err) {
+                log(`Warning: cannot verify the checkpoint against the store (getDistinctPaths failed: ${err instanceof Error ? err.message : String(err)}) — re-embedding everything without trusting the checkpoint.`);
+            }
+            const epochStart = resumeFrom.startedAt;
+            const byRel = new Map(allFiles.map((f) => [normalizeRel(f.relativePath), f]));
+            const tracked = new Set(detailed.tracked.map(normalizeRel));
+            const movedSinceEpoch = (rel) => {
+                if (tracked.has(rel))
+                    return true;
+                const file = byRel.get(rel);
+                if (!file)
+                    return true;
+                try {
+                    return fs.statSync(file.absolutePath).mtimeMs > epochStart;
+                    // totem-context: intentional treat-as-moved on a stat failure (mmnto-ai/totem#2562) — the file re-embeds (idempotent via delete-first) or the read site skips a vanished file loudly.
+                }
+                catch {
+                    return true;
+                }
+            };
+            const indexed = indexedRaw === null ? null : new Set(indexedRaw.map(normalizeRel));
+            const completed = new Set(indexed === null
+                ? []
+                : resumeFrom.completedFiles
+                    .map(normalizeRel)
+                    .filter((rel) => byRel.has(rel) && indexed.has(rel) && !movedSinceEpoch(rel)));
+            filesToProcess = allFiles.filter((f) => !completed.has(normalizeRel(f.relativePath)));
+            // EFFECTIVE-vs-effective identity gate (falsification rounds 2–4). The
+            // epoch may only continue under the embedder identity that will
+            // ACTUALLY serve this run's embeds — config-vs-stamped is wrong in both
+            // directions (a silent fallback would mix vector spaces at the first
+            // insert; a persistent fallback would restart-loop forever). The
+            // exemption is RESOLUTION FAILURE with zero work remaining (round 3
+            // MINOR 10: an epoch that merely needs its marker cleared must not
+            // wedge behind a missing embedder) — NOT zero work itself: a resolvable
+            // mismatch must restart even with nothing left, or clearing the marker
+            // would rewrite index-meta to the new identity and launder the
+            // DATABASE_MISMATCH evidence the next incremental needs (round 4,
+            // MAJOR 1 — probed: dimension change + zero-work resume ⇒ silent mixed
+            // store).
+            let identityOk = true;
+            let effectiveNow = null;
+            try {
+                effectiveNow = (await embedder.resolveEffective?.()) ?? embedderFingerprint;
+            }
+            catch (err) {
+                if (filesToProcess.length > 0)
+                    throw err; // work remains ⇒ fail loud, state intact
+                log(`Nothing left to embed and no embedder resolved (${err instanceof Error ? err.message : String(err)}) — clearing the marker unverified.`);
+            }
+            if (effectiveNow !== null) {
+                const fp = resumeFrom.embedder;
+                if (fp.provider !== effectiveNow.provider ||
+                    fp.model !== effectiveNow.model ||
+                    fp.dimensions !== effectiveNow.dimensions) {
+                    log(`The embedder serving this run (${effectiveNow.provider}/${effectiveNow.model}) differs from the interrupted epoch's (${fp.provider}/${fp.model}) — its progress is unusable; restarting from zero.`);
+                    identityOk = false;
+                }
+            }
+            if (!identityOk) {
+                await beginFullSync(freshCheckpoint());
+                filesToProcess = allFiles;
+                log(`Full sync: ${filesToProcess.length} files to process`);
+            }
+            else {
+                // Carry forward the verified entries, re-keyed to the current run's
+                // resolved paths — EXCEPT when the store was unreadable: then the
+                // paper progress is retained untrusted (round 3, MINOR 9a) so a
+                // second crash does not erase a prior epoch's flushed work; the next
+                // resume re-verifies it against a hopefully-readable store.
+                // startedHeadSha stays the ORIGINAL epoch SHA so every later resume
+                // re-diffs the full window (superset-safe).
+                const carried = indexed === null
+                    ? [...resumeFrom.completedFiles]
+                    : allFiles.map((f) => f.relativePath).filter((rel) => completed.has(normalizeRel(rel)));
+                checkpoint = { ...resumeFrom, indexExclusionHash, completedFiles: carried };
+                writeFullSyncCheckpoint(totemDir, checkpoint);
+                resumedWithoutReset = true;
+                log(`Resuming full re-index: ${filesToProcess.length} file(s) remaining of ${allFiles.length} ` +
+                    `(${completed.size} verified already embedded). Delete ${config.totemDir}/${FULL_SYNC_CHECKPOINT_FILE} to restart from scratch.`);
+            }
+        }
+    }
     else {
-        log('Full sync: resetting index...');
-        await store.reset();
+        await beginFullSync(freshCheckpoint());
         filesToProcess = allFiles;
         log(`Full sync: ${filesToProcess.length} files to process`);
     }
@@ -288,6 +516,7 @@ async function runSyncInner(config, options) {
     // 4. Chunk files and stream to LanceDB in batches (bounded memory)
     let totalChunks = 0;
     let buffer = [];
+    let pendingFiles = [];
     async function flushBuffer() {
         if (buffer.length === 0)
             return;
@@ -295,21 +524,71 @@ async function runSyncInner(config, options) {
         totalChunks += buffer.length;
         log(`  Embedded ${totalChunks} chunks so far`);
         buffer = [];
+        // #2562: chunks buffer at whole-file boundaries and store.insert embeds
+        // before any row lands, so a successful flush means every pending file is
+        // complete in the store — checkpoint them. An append failure is
+        // survivable: the file re-embeds on resume via the delete-first path.
+        const cp = checkpoint;
+        if (cp && pendingFiles.length > 0) {
+            cp.completedFiles.push(...pendingFiles);
+            // Persist the EFFECTIVE embedder identity once known (falsification
+            // round 1, MAJOR 3): a LazyEmbedder that silently fell back to Ollama
+            // must not leave a checkpoint fingerprinted as the configured provider,
+            // or the next resume would mix vector spaces across the epoch.
+            const effective = embedder.describeEffective?.();
+            if (effective)
+                cp.embedder = effective;
+            try {
+                writeFullSyncCheckpoint(totemDir, cp);
+                // totem-context: intentional warn+continue on a checkpoint-append failure (mmnto-ai/totem#2562) — the flushed chunks are safe in the store; worst case the file re-embeds on resume via the delete-first path.
+            }
+            catch (err) {
+                log(`  Warning: failed to update full-sync checkpoint: ${err instanceof Error ? err.message : String(err)}`);
+            }
+        }
+        pendingFiles = [];
     }
     for (const file of filesToProcess) {
         const safeRel = sanitizeForTerminal(file.relativePath);
         log(`Chunking ${safeRel}...`);
+        // A file whose CURRENT state legitimately yields no rows (emptied of
+        // chunkable content, or swapped to a symlink the guard refuses) must
+        // still purge its OLD rows when re-processing in place — the baseline
+        // advances past the change at the end of this run, so no later
+        // incremental diff revisits it and the stale rows would be searchable
+        // forever (#2569 Greptile round: stale-rows-on-skip). The transient
+        // read-error skip below deliberately does NOT purge: deleting on a
+        // maybe-transient failure would LOSE good rows, worse than stale ones.
+        const purgeStaleRows = async () => {
+            if (incremental || resumedWithoutReset) {
+                await store.deleteByFile(file.relativePath);
+            }
+        };
+        // Symlink guard at the READ site (mmnto-ai/totem#2354, #2356 review):
+        // resolveFiles skips symlinks at discovery, but this read happens later,
+        // so a path swapped to a symlink after resolution would still be followed
+        // by readFileSync. Re-check here and skip — closes the discovery→read
+        // TOCTOU gap. The purge runs OUTSIDE the read-error catches (#2569 CR
+        // round 2): caught there, a purge failure would be mislabeled a read
+        // error and silently downgraded to a skip — permanent staleness. Outside
+        // them it fails loud and CONVERGES: the marker/stale baseline makes the
+        // next run re-evict the file and retry the delete.
+        let isSymlink;
+        try {
+            isSymlink = fs.lstatSync(file.absolutePath).isSymbolicLink();
+            // totem-context: intentional skip — a per-file stat failure (vanished/raced file, permission) logs and skips just that file so sync continues over the rest; aborting the whole sync over one unreadable file would be the drift, not the skip.
+        }
+        catch (err) {
+            log(`  Skipping (read error: ${sanitizeForTerminal(err instanceof Error ? err.message : String(err))}): ${safeRel}`);
+            continue;
+        }
+        if (isSymlink) {
+            log(`  Skipping symlink (not indexed): ${safeRel}`);
+            await purgeStaleRows();
+            continue;
+        }
         let content;
         try {
-            // Symlink guard at the READ site (mmnto-ai/totem#2354, #2356 review):
-            // resolveFiles skips symlinks at discovery, but this read happens later,
-            // so a path swapped to a symlink after resolution would still be followed
-            // by readFileSync. Re-check here and skip — closes the discovery→read
-            // TOCTOU gap.
-            if (fs.lstatSync(file.absolutePath).isSymbolicLink()) {
-                log(`  Skipping symlink (not indexed): ${safeRel}`);
-                continue;
-            }
             content = fs.readFileSync(file.absolutePath, 'utf-8');
             // totem-context: intentional skip — a per-file read failure (vanished/raced file, permission, decode) logs and skips just that file so sync continues over the rest; aborting the whole sync over one unreadable file would be the drift, not the skip.
         }
@@ -321,12 +600,14 @@ async function runSyncInner(config, options) {
         const chunks = chunker.chunk(content, file.relativePath, file.target.type);
         if (chunks.length === 0) {
             log(`  No chunks extracted from ${file.relativePath}`);
+            await purgeStaleRows();
             continue;
         }
-        // For incremental: delete old chunks for this file before inserting new ones
-        if (incremental) {
-            await store.deleteByFile(file.relativePath);
-        }
+        // Delete old chunks for this file before inserting new ones — incremental
+        // re-embeds in place, and a #2562 resume (no reset) can hold this file's
+        // chunks already (changed-since-epoch, or a flush whose checkpoint append
+        // failed). Idempotent either way.
+        await purgeStaleRows();
         // Sanitize chunk content before embedding (adversarial ingestion scrubbing)
         // Deduplicate warnings per file to avoid log spam on files with widespread issues
         const warnedMessages = new Set();
@@ -346,6 +627,7 @@ async function runSyncInner(config, options) {
             chunk.contextPrefix = sanitizeForIngestion(chunk.contextPrefix, sanitizeOpts);
         }
         buffer.push(...chunks);
+        pendingFiles.push(file.relativePath);
         log(`  ${chunks.length} chunks from ${file.relativePath}`);
         // Flush when buffer reaches batch size to keep memory bounded
         if (buffer.length >= EMBED_BATCH_SIZE) {
@@ -372,6 +654,13 @@ async function runSyncInner(config, options) {
     if (headSha) {
         writeSyncState(totemDir, { lastSyncSha: headSha, timestamp: Date.now(), indexExclusionHash });
     }
+    // #2562: the epoch is complete — clear the dirty marker only AFTER the fresh
+    // baseline is on disk. A crash between the two writes leaves marker + fresh
+    // baseline, which the next run resumes as a near-noop; the reverse order
+    // would leave a clean-claiming baseline over a still-marked store.
+    if (checkpoint) {
+        deleteFullSyncCheckpoint(totemDir, log);
+    }
     // Persist index metadata for dimension mismatch detection
     writeIndexMeta(totemDir, {
         provider: embedding.provider,
@@ -386,10 +675,7 @@ async function runSyncInner(config, options) {
         const writtenAt = new Date();
         const docs = await store.manifestDocuments(writtenAt);
         const manifest = buildIndexManifest({ documents: docs, headSha, writtenAt });
-        const manifestPath = path.join(totemDir, 'index-manifest.json');
-        const tmpManifestPath = manifestPath + '.tmp';
-        fs.writeFileSync(tmpManifestPath, JSON.stringify(manifest, null, 2) + '\n', 'utf-8');
-        fs.renameSync(tmpManifestPath, manifestPath);
+        writeJsonAtomic(path.join(totemDir, 'index-manifest.json'), manifest);
     }
     catch (err) {
         const detail = err instanceof Error ? err.message : typeof err === 'string' ? err : 'unknown error';

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