@nxuss/lemma 1.19.0 → 1.21.0

package/dist/cjs/subconscious/TheBrainV2.d.ts

@@ -176,8 +176,15 @@ export interface ClaimFreshness {
  * gets for a purged entry, a renamed symbol's old claim, or an id from another project.
  */
 export interface VerifyMemoryResult {
+    /**
+     * 'fresh' means every tracked artifact still hashes the same. 'untracked' means the memory
+     * tracks nothing at all, so there was nothing to check — never folded into 'fresh', because
+     * a caller reading 'fresh' is being told the memory was validated against current code.
+     */
+    status: 'fresh' | 'stale' | 'unverified' | 'unknown' | 'untracked';
     id: string;
-    status: 'fresh' | 'stale' | 'unverified' | 'unknown';
+    /** Files/symbols/upstream memories this id is judged against. 0 on 'untracked'. */
+    trackedArtifacts?: number;
     staleFiles?: string[];
     /** Only set when `id` resolved to an entry that itself has per-claim tracking. */
     claimBreakdown?: ClaimFreshness[];
@@ -287,6 +294,12 @@ export interface BrainStats {
     staleEntries?: number;
     /** Only under { deep: true }: staleEntries as a fraction of entries that track anything. */
     staleRatio?: number;
+    /**
+     * Entries tracking no file, symbol, claim evidence or upstream memory at all — the ones
+     * `verify_memory` reports as `untracked` because there is nothing there to check. Cheap
+     * (no hashing), so it is always computed, unlike staleEntries.
+     */
+    untrackedEntries?: number;
 }
 /**
  * Union two views of the corpus. Never subtracts: an id present in either side survives
@@ -419,6 +432,18 @@ export interface FreshnessOutcome {
  * `fresh`.
  */
 export declare function checkEntryFreshness(entry: BrainEntry, resolver: EvidenceResolver, resolveNode?: (id: string) => FreshnessNode | undefined, depth?: number, visited?: Set<string>, semanticDiff?: boolean): FreshnessOutcome;
+/**
+ * How many artifacts an entry's freshness is actually judged against: tracked files, tracked
+ * symbols, upstream memories, and each claim's own evidence.
+ *
+ * Zero means a freshness check has nothing to compare — and reporting that as `fresh` conflates
+ * "validated against the code" with "there was nothing to validate", which are opposite
+ * guarantees for a caller about to act on the memory. `verify_memory` reports those as
+ * `untracked` instead; see VerifyMemoryResult.
+ */
+export declare function trackedArtifactCount(entry: BrainEntry): number;
+/** Claim-level counterpart to trackedArtifactCount. */
+export declare function trackedClaimArtifactCount(claim: Claim): number;
 /**
  * Same hash-compare as checkEntryFreshness, scoped to one claim's own evidence — a claim
  * with no fileHashes/symbolHashes at all is always fresh (nothing tracked to go stale).
@@ -439,9 +464,20 @@ export declare class TheBrainV2 {
     private diskStamp;
     /** id -> ISO deletion time, for ids that must not come back through a merge. */
     private tombstones;
+    /**
+     * id -> terms of that entry's own `query` field. Derived state, never persisted: `terms`
+     * covers query+response together, so scoring the query field on its own (see the
+     * QUERY_FIELD_BOOST block in search()) needs it split back out. Memoized because a search
+     * touches every candidate and re-tokenizing a prompt per candidate per search is pure waste.
+     * Dropped whenever the entry changes or leaves the corpus — a stale entry here would boost
+     * a memory for words its prompt no longer contains.
+     */
+    private queryTermCache;
     constructor();
     private ensureDir;
     private load;
+    /** Terms of an entry's own `query`, memoized. See queryTermCache. */
+    private queryTermsOf;
     /** Recomputes the inverted index from scratch over the current entries. */
     private rebuildIndex;
     /**
@@ -551,6 +587,28 @@ export declare class TheBrainV2 {
      * without deleting the entry — a bad-fit-today memory may still be exactly right for a
      * differently-phrased query tomorrow.
      */
+    /**
+     * One memory, by id, body included.
+     *
+     * The Brain had no deterministic read: `verifyByIds` answers "is it still true" without
+     * returning the text, and `search()` — the only path to the body — is a ranking, so an agent
+     * holding an id could still fail to retrieve the memory it had just written. Editing a
+     * long-lived entry under those conditions means reconstructing its text from whatever a
+     * search happened to surface, which is how the accumulated content in it gets lost.
+     *
+     * Returns a copy: callers must not mutate the corpus by holding a reference. Use update()
+     * to change a memory.
+     */
+    getEntry(id: string): BrainEntry | undefined;
+    /**
+     * The entry a claim id belongs to, plus the claim itself. Claim ids and entry ids are handed
+     * back side by side by search_memory and verify_memory, so an id pasted into a read is as
+     * likely to be one as the other — resolving only entries would report a live claim as missing.
+     */
+    getClaim(id: string): {
+        entry: BrainEntry;
+        claim: Claim;
+    } | undefined;
     downvote(id: string): {
         ok: boolean;
         message: string;
@@ -575,9 +633,11 @@ export declare class TheBrainV2 {
         forgotten?: {
             id: string;
             query: string;
+            response: string;
             timestamp: string;
             hits: number;
         };
+        archivePath?: string;
     };
     /**
      * Re-verify a memory against the code as it stands now, keeping its identity.
@@ -598,6 +658,13 @@ export declare class TheBrainV2 {
      * a memory that is itself stale is exactly what Fase B exists to catch, and silently
      * clearing that would defeat it. Those come back in `stillStale` instead.
      */
+    /**
+     * Re-hash an entry's evidence, either in place or against newly named files/symbols.
+     * Shared by refresh() ("I checked, this is still true") and update() ("here is the corrected
+     * text"), which make the same assertion about the same code and so must anchor identically.
+     * Mutates `entry`; returns the labels of what it now tracks.
+     */
+    private reanchorEvidence;
     refresh(id: string, opts?: {
         filePaths?: string[];
         symbols?: SymbolRef[];
@@ -608,6 +675,40 @@ export declare class TheBrainV2 {
         retracked?: string[];
         stillStale?: string[];
     };
+    /**
+     * Replace an existing memory's content, keeping its identity.
+     *
+     * The Brain could add and it could delete, but it could not correct: store() mints a new id
+     * per call, so re-storing a corrected version under the same query left the outdated one in
+     * place, and a later search returned an arbitrary slice of every historical version —
+     * including the ones that contradict each other. That is the mechanism behind an
+     * append-only pile of near-duplicate "canonical index" entries: not a convention nobody
+     * followed, a convention the API could not express. refresh() keeps identity but only
+     * re-hashes evidence, and has no way to accept new text. This is that missing operation.
+     *
+     * Kept: id, hits, demerits, creation timestamp, projectId, source, and every `derivedFrom`
+     * edge elsewhere in the corpus that points at this id. Replaced: whatever the patch names.
+     * Evidence is re-anchored exactly as refresh() does — rewriting a memory's content asserts
+     * the same thing refresh() records, that the caller checked it against the code as it is now.
+     */
+    update(id: string, patch?: {
+        query?: string;
+        response?: string;
+        filePaths?: string[];
+        symbols?: SymbolRef[];
+        claims?: ClaimInput[];
+        outcome?: 'confirmed' | 'failed';
+        domain?: string;
+        derivedFrom?: string[];
+    }): {
+        ok: boolean;
+        message: string;
+        id?: string;
+        fresh?: boolean;
+        retracked?: string[];
+        stillStale?: string[];
+        charDelta?: number;
+    };
     /**
      * Revalidate ids from a prior search_memory/store_memory result via hash-compare only —
      * no BM25, no `search()`. `ids` may mix entry ids and claim ids freely; each resolves

package/dist/cjs/subconscious/TheBrainV2.d.ts.map

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package/dist/cjs/subconscious/TheBrainV2.js

@@ -29,6 +29,8 @@ exports.resolveFreshnessNode = resolveFreshnessNode;
 exports.buildClaimIndex = buildClaimIndex;
 exports.findBlastRadius = findBlastRadius;
 exports.checkEntryFreshness = checkEntryFreshness;
+exports.trackedArtifactCount = trackedArtifactCount;
+exports.trackedClaimArtifactCount = trackedClaimArtifactCount;
 exports.checkClaimFreshness = checkClaimFreshness;
 exports.getBrain = getBrain;
 const fs_1 = __importDefault(require("fs"));
@@ -48,6 +50,15 @@ const defaultLocalResolver = new LocalFsResolver_1.LocalFsResolver();
 // ─── BM25 Constants ───────────────────────────────────────────────────────────
 const BM25_K1 = 1.5; // Term saturation (1.2-2.0)
 const BM25_B = 0.75; // Length normalization (0-1)
+/**
+ * Ceiling on the document-length term in BM25's normalization, in multiples of the average
+ * document. Uncapped, the divisor grows with the document forever, so a memory is buried for
+ * being long rather than for being a worse match — which is precisely what happened to the
+ * one entry a "living document" convention keeps rewriting and growing: it ranked below the
+ * 2 KB fragments it was written to supersede, under its own query. Past 3x average, extra
+ * length says nothing more about relevance, so the penalty stops there.
+ */
+const MAX_LENGTH_NORM_RATIO = 3;
 // ─── Recency decay ────────────────────────────────────────────────────────────
 //
 // Deliberately gentle and grace-periodded. Age is a weak proxy for "no longer true" —
@@ -61,6 +72,18 @@ const RECENCY_GRACE_DAYS = 30;
 const RECENCY_FULL_DECAY_DAYS = 365;
 /** Cap, in the same 0-1 similarity space as the popularity/outcome/demerit adjustments. */
 const MAX_RECENCY_PENALTY = 0.10;
+// ─── Retrieval blend ──────────────────────────────────────────────────────────
+//
+// Three signals, weights summing to 1 so the blend stays a 0-1 similarity the caller can hold
+// against a floor. The third is new: an entry's `terms` cover query and response together, so
+// "these words are the memory's own prompt" scored exactly like "these words appear somewhere
+// in a long body", and a document that keeps growing dilutes its own prompt out of contention.
+// That is a retrieval signal, not a tie-break like the small additive adjustments in search(),
+// so it takes its share of the blend rather than being added on top of it.
+const BM25_WEIGHT = 0.55;
+const JACCARD_WEIGHT = 0.20;
+/** Share of the blend decided by how much of the search query the entry's own query covers. */
+const QUERY_FIELD_WEIGHT = 0.25;
 // ─── Storage Paths ────────────────────────────────────────────────────────────
 /**
  * LEMMA_BRAIN_DIR redirects storage — required so tests never write into the user's real
@@ -75,6 +98,14 @@ const META_FILE = path_1.default.join(BRAIN_DIR, 'meta.json');
 const LOCK_FILE = path_1.default.join(BRAIN_DIR, '.write.lock');
 /** Sidecar vector cache for the optional semantic re-rank. See BrainEmbeddings.ts. */
 const EMBEDDINGS_FILE = path_1.default.join(BRAIN_DIR, 'embeddings.ndjson');
+/**
+ * Append-only archive of everything forget() destroyed. Deletion is the one Brain operation
+ * with no undo, and the deleted body is by definition the only copy of that text — telling the
+ * caller "nothing else can recover it" and then handing back metadata only is the worst of both
+ * worlds. The id stays tombstoned (a deliberate deletion must not come back through a merge),
+ * so this file is an archive to read, not a bundle to re-import.
+ */
+const FORGOTTEN_FILE = path_1.default.join(BRAIN_DIR, 'forgotten.ndjson');
 // ─── Cross-process durability ─────────────────────────────────────────────────
 //
 // Every MCP client session starts its own server process, and each one holds the whole
@@ -549,13 +580,16 @@ exports.BloomFilter = BloomFilter;
 // ─── BM25 Scorer ─────────────────────────────────────────────────────────────
 function bm25Score(queryTerms, docTermFreq, docLength, avgDocLength, idf) {
     let score = 0;
+    // Bounded: see MAX_LENGTH_NORM_RATIO. A document 20x the average was effectively
+    // unretrievable next to a short one sharing the same rare term.
+    const lengthRatio = Math.min(docLength / avgDocLength, MAX_LENGTH_NORM_RATIO);
     for (const term of queryTerms) {
         if (!(term in docTermFreq))
             continue;
         const tf = docTermFreq[term];
         const termIdf = idf[term] || 0;
         const numerator = tf * (BM25_K1 + 1);
-        const denominator = tf + BM25_K1 * (1 - BM25_B + BM25_B * (docLength / avgDocLength));
+        const denominator = tf + BM25_K1 * (1 - BM25_B + BM25_B * lengthRatio);
         score += termIdf * (numerator / denominator);
     }
     return score;
@@ -856,6 +890,28 @@ function checkEntryFreshness(entry, resolver, resolveNode, depth = 0, visited =
         ...(cosmeticChanges.length > 0 ? { cosmeticChanges } : {}),
     };
 }
+/**
+ * How many artifacts an entry's freshness is actually judged against: tracked files, tracked
+ * symbols, upstream memories, and each claim's own evidence.
+ *
+ * Zero means a freshness check has nothing to compare — and reporting that as `fresh` conflates
+ * "validated against the code" with "there was nothing to validate", which are opposite
+ * guarantees for a caller about to act on the memory. `verify_memory` reports those as
+ * `untracked` instead; see VerifyMemoryResult.
+ */
+function trackedArtifactCount(entry) {
+    let n = Object.keys(entry.fileHashes || {}).length;
+    n += Object.keys(entry.symbolHashes || {}).length;
+    n += (entry.derivedFrom || []).length;
+    for (const claim of entry.claims || []) {
+        n += Object.keys(claim.fileHashes || {}).length + Object.keys(claim.symbolHashes || {}).length;
+    }
+    return n;
+}
+/** Claim-level counterpart to trackedArtifactCount. */
+function trackedClaimArtifactCount(claim) {
+    return Object.keys(claim.fileHashes || {}).length + Object.keys(claim.symbolHashes || {}).length;
+}
 /** Builds the persisted `Claim[]` for an entry from the caller-supplied claim inputs. */
 function buildClaims(inputs) {
     return inputs
@@ -944,6 +1000,15 @@ class TheBrainV2 {
         this.diskStamp = null;
         /** id -> ISO deletion time, for ids that must not come back through a merge. */
         this.tombstones = new Map();
+        /**
+         * id -> terms of that entry's own `query` field. Derived state, never persisted: `terms`
+         * covers query+response together, so scoring the query field on its own (see the
+         * QUERY_FIELD_BOOST block in search()) needs it split back out. Memoized because a search
+         * touches every candidate and re-tokenizing a prompt per candidate per search is pure waste.
+         * Dropped whenever the entry changes or leaves the corpus — a stale entry here would boost
+         * a memory for words its prompt no longer contains.
+         */
+        this.queryTermCache = new Map();
         this.sidecar = null;
         this.ensureDir();
         this.load();
@@ -982,9 +1047,21 @@ class TheBrainV2 {
             this.tombstones = new Map();
         }
     }
+    /** Terms of an entry's own `query`, memoized. See queryTermCache. */
+    queryTermsOf(entry) {
+        let set = this.queryTermCache.get(entry.id);
+        if (!set) {
+            set = new Set(tokenize(entry.query));
+            this.queryTermCache.set(entry.id, set);
+        }
+        return set;
+    }
     /** Recomputes the inverted index from scratch over the current entries. */
     rebuildIndex() {
         this.invertedIndex = new Map();
+        // A merge can replace an id's entry with a peer's newer version whose query differs, so
+        // the memo is rebuilt alongside the index rather than trusted across one.
+        this.queryTermCache.clear();
         for (const entry of this.entries.values()) {
             for (const term of entry.terms) {
                 let ids = this.invertedIndex.get(term);
@@ -1133,6 +1210,7 @@ class TheBrainV2 {
     /** Removes an entry from the in-memory corpus and the inverted index. No persistence. */
     dropEntry(entry) {
         this.entries.delete(entry.id);
+        this.queryTermCache.delete(entry.id);
         for (const term of entry.terms) {
             const ids = this.invertedIndex.get(term);
             if (!ids)
@@ -1354,8 +1432,24 @@ class TheBrainV2 {
         // see on their own: a memory's own track record. Small and additive by design — none of
         // these can turn an unrelated result into a top hit, they only reorder among already-
         // relevant candidates.
+        const normalizedQuery = query.trim().toLowerCase();
         const combined = scored.map(s => {
-            let similarity = (s.bm25 / maxBm25) * 0.7 + s.jaccard * 0.3;
+            // How much of the search query appears in the entry's own prompt — see the weights above.
+            const entryQueryTerms = this.queryTermsOf(s.entry);
+            let covered = 0;
+            for (const term of queryTermSet)
+                if (entryQueryTerms.has(term))
+                    covered++;
+            const queryFieldMatch = covered / queryTermSet.size;
+            // A prompt that matches character for character is not one signal among three — it is
+            // the entry filed under exactly this question. Blended, it could still lose to a short
+            // fragment that repeated one rare term, which is how a memory became unfindable under
+            // its own query. The adjustments below still apply on top: a downvoted or dead-end
+            // exact match must not outrank a clean one.
+            const exactPrompt = s.entry.query.trim().toLowerCase() === normalizedQuery;
+            let similarity = exactPrompt
+                ? 1
+                : (s.bm25 / maxBm25) * BM25_WEIGHT + s.jaccard * JACCARD_WEIGHT + queryFieldMatch * QUERY_FIELD_WEIGHT;
             // Popularity prior: entries other searches actually reused are more likely to be
             // reused again. Log-scaled and capped at +0.08 so a handful of hits can't outrank a
             // much better textual match.
@@ -1542,6 +1636,38 @@ class TheBrainV2 {
      * without deleting the entry — a bad-fit-today memory may still be exactly right for a
      * differently-phrased query tomorrow.
      */
+    // ─── Read by id ─────────────────────────────────────────────────────────────
+    /**
+     * One memory, by id, body included.
+     *
+     * The Brain had no deterministic read: `verifyByIds` answers "is it still true" without
+     * returning the text, and `search()` — the only path to the body — is a ranking, so an agent
+     * holding an id could still fail to retrieve the memory it had just written. Editing a
+     * long-lived entry under those conditions means reconstructing its text from whatever a
+     * search happened to surface, which is how the accumulated content in it gets lost.
+     *
+     * Returns a copy: callers must not mutate the corpus by holding a reference. Use update()
+     * to change a memory.
+     */
+    getEntry(id) {
+        this.syncIfChanged();
+        const entry = this.entries.get(id);
+        return entry ? { ...entry } : undefined;
+    }
+    /**
+     * The entry a claim id belongs to, plus the claim itself. Claim ids and entry ids are handed
+     * back side by side by search_memory and verify_memory, so an id pasted into a read is as
+     * likely to be one as the other — resolving only entries would report a live claim as missing.
+     */
+    getClaim(id) {
+        this.syncIfChanged();
+        for (const entry of this.entries.values()) {
+            const claim = entry.claims?.find((c) => c.id === id);
+            if (claim)
+                return { entry: { ...entry }, claim };
+        }
+        return undefined;
+    }
     downvote(id) {
         this.syncIfChanged();
         const entry = this.entries.get(id);
@@ -1571,6 +1697,19 @@ class TheBrainV2 {
         const entry = this.entries.get(id);
         if (!entry)
             return { ok: false, message: `No entry with id "${id}" in the Brain.` };
+        // Archived before it is dropped: the body is the only copy of that text anywhere, and
+        // "nothing else can recover it" has to be a description of the archive, not of a gap.
+        let archivePath;
+        try {
+            this.ensureDir();
+            const { terms: _terms, ...persisted } = entry;
+            fs_1.default.appendFileSync(FORGOTTEN_FILE, JSON.stringify({ ...persisted, forgottenAt: new Date().toISOString() }) + '\n', 'utf8');
+            archivePath = FORGOTTEN_FILE;
+        }
+        catch {
+            // An unwritable archive must not block a deletion the user asked for — the body still
+            // comes back in the result below, which is the copy that matters in the moment.
+        }
         this.dropEntry(entry);
         this.tombstone(id);
         this.recalcAvgDocLength();
@@ -1580,7 +1719,10 @@ class TheBrainV2 {
             message: `Deleted memory "${id}". It will not come back from another session's copy.`,
             // Echoed back so a deletion is auditable: the caller (and the user reading the
             // transcript) can see exactly what was destroyed, since nothing else can recover it.
-            forgotten: { id, query: entry.query, timestamp: entry.timestamp, hits: entry.hits },
+            // The response is included, not just its metadata — a record of a deletion that omits
+            // the deleted content is not a record of anything.
+            forgotten: { id, query: entry.query, response: entry.response, timestamp: entry.timestamp, hits: entry.hits },
+            ...(archivePath ? { archivePath } : {}),
         };
     }
     // ─── Re-anchoring ───────────────────────────────────────────────────────────
@@ -1603,11 +1745,13 @@ class TheBrainV2 {
      * a memory that is itself stale is exactly what Fase B exists to catch, and silently
      * clearing that would defeat it. Those come back in `stillStale` instead.
      */
-    refresh(id, opts = {}) {
-        this.syncIfChanged();
-        const entry = this.entries.get(id);
-        if (!entry)
-            return { ok: false, message: `No entry with id "${id}" in the Brain.` };
+    /**
+     * Re-hash an entry's evidence, either in place or against newly named files/symbols.
+     * Shared by refresh() ("I checked, this is still true") and update() ("here is the corrected
+     * text"), which make the same assertion about the same code and so must anchor identically.
+     * Mutates `entry`; returns the labels of what it now tracks.
+     */
+    reanchorEvidence(entry, opts) {
         const retracked = [];
         const rel = (abs) => {
             const r = path_1.default.relative(process.cwd(), abs);
@@ -1660,6 +1804,14 @@ class TheBrainV2 {
                 }
             }
         }
+        return retracked;
+    }
+    refresh(id, opts = {}) {
+        this.syncIfChanged();
+        const entry = this.entries.get(id);
+        if (!entry)
+            return { ok: false, message: `No entry with id "${id}" in the Brain.` };
+        const retracked = this.reanchorEvidence(entry, opts);
         // Re-stamp git context and the age clock: this memory was just re-verified here, now.
         const git = currentGitContext();
         if (git.commit)
@@ -1681,6 +1833,89 @@ class TheBrainV2 {
                     `A "derived:" entry here means an upstream memory it was built on is stale — refresh that one first.`,
         };
     }
+    // ─── In-place rewrite ───────────────────────────────────────────────────────
+    /**
+     * Replace an existing memory's content, keeping its identity.
+     *
+     * The Brain could add and it could delete, but it could not correct: store() mints a new id
+     * per call, so re-storing a corrected version under the same query left the outdated one in
+     * place, and a later search returned an arbitrary slice of every historical version —
+     * including the ones that contradict each other. That is the mechanism behind an
+     * append-only pile of near-duplicate "canonical index" entries: not a convention nobody
+     * followed, a convention the API could not express. refresh() keeps identity but only
+     * re-hashes evidence, and has no way to accept new text. This is that missing operation.
+     *
+     * Kept: id, hits, demerits, creation timestamp, projectId, source, and every `derivedFrom`
+     * edge elsewhere in the corpus that points at this id. Replaced: whatever the patch names.
+     * Evidence is re-anchored exactly as refresh() does — rewriting a memory's content asserts
+     * the same thing refresh() records, that the caller checked it against the code as it is now.
+     */
+    update(id, patch = {}) {
+        this.syncIfChanged();
+        const entry = this.entries.get(id);
+        if (!entry)
+            return { ok: false, message: `No entry with id "${id}" in the Brain.` };
+        const beforeChars = entry.charCount;
+        // Out of the index before its terms change: a posting list built from the old text would
+        // keep serving this entry under words the new text no longer contains.
+        this.dropEntry(entry);
+        if (typeof patch.query === 'string' && patch.query.trim())
+            entry.query = patch.query.trim();
+        if (typeof patch.response === 'string' && patch.response.trim())
+            entry.response = patch.response.trim();
+        if (patch.outcome)
+            entry.outcome = patch.outcome;
+        if (patch.domain !== undefined)
+            entry.domain = patch.domain.trim() || undefined;
+        if (patch.derivedFrom !== undefined) {
+            entry.derivedFrom = patch.derivedFrom.length > 0 ? patch.derivedFrom : undefined;
+        }
+        if (patch.claims !== undefined) {
+            entry.claims = patch.claims.length > 0 ? buildClaims(patch.claims) : undefined;
+        }
+        const terms = tokenize(entry.query + ' ' + entry.response);
+        entry.terms = [...new Set(terms)];
+        entry.termFreq = termFrequencies(terms);
+        entry.charCount = entry.query.length + entry.response.length;
+        // Claims supplied in this patch were just hashed by buildClaims; the helper re-anchors the
+        // ones carried over, so either way the entry's evidence describes the code as it is now.
+        const retracked = this.reanchorEvidence(entry, { filePaths: patch.filePaths, symbols: patch.symbols });
+        const git = currentGitContext();
+        if (git.commit)
+            entry.gitCommit = git.commit;
+        if (git.branch)
+            entry.gitBranch = git.branch;
+        // Same clock reset as refresh(): re-verified content really is current again. `timestamp`
+        // is left alone so provenance is never rewritten.
+        entry.refreshedAt = new Date().toISOString();
+        this.entries.set(id, entry);
+        for (const term of entry.terms) {
+            let ids = this.invertedIndex.get(term);
+            if (!ids) {
+                ids = new Set();
+                this.invertedIndex.set(term, ids);
+            }
+            ids.add(id);
+        }
+        this.bloom.add(entry.query.trim().toLowerCase().substring(0, 200));
+        this.recalcAvgDocLength();
+        this.scheduleSave();
+        const claimIndex = buildClaimIndex(this.entries);
+        const { fresh, staleFiles } = checkEntryFreshness(entry, defaultLocalResolver, (depId) => resolveFreshnessNode(this.entries, claimIndex, depId));
+        const charDelta = entry.charCount - beforeChars;
+        return {
+            ok: true,
+            id,
+            fresh,
+            retracked,
+            charDelta,
+            ...(staleFiles.length > 0 ? { stillStale: staleFiles } : {}),
+            message: fresh
+                ? `Memory "${id}" updated in place, keeping its id, ${entry.hits} hit(s) and every derivedFrom edge pointing at it.`
+                : `Memory "${id}" updated in place, but still stale: ${staleFiles.join(', ')}. ` +
+                    `A "derived:" entry here means an upstream memory it was built on is stale — refresh that one first.`,
+        };
+    }
     // ─── Batch verification ─────────────────────────────────────────────────────
     /**
      * Revalidate ids from a prior search_memory/store_memory result via hash-compare only —
@@ -1704,9 +1939,13 @@ class TheBrainV2 {
             if (entry) {
                 const { fresh, staleFiles, unverifiedFiles, cosmeticChanges } = checkEntryFreshness(entry, resolver, resolveNode, 0, new Set(), semanticDiff);
                 const unverified = unverifiedFiles.length > 0;
+                // An entry that tracks nothing cannot be checked, and saying 'fresh' would answer a
+                // question ("does this still match the code?") that was never asked of it.
+                const tracked = trackedArtifactCount(entry);
                 return {
                     id,
-                    status: unverified ? 'unverified' : fresh ? 'fresh' : 'stale',
+                    status: unverified ? 'unverified' : !fresh ? 'stale' : tracked === 0 ? 'untracked' : 'fresh',
+                    trackedArtifacts: tracked,
                     ...(unverified || fresh ? {} : attributeStaleness(entry, git)),
                     ...(staleFiles.length > 0 ? { staleFiles } : {}),
                     ...(unverified ? { unverifiedFiles } : {}),
@@ -1718,9 +1957,11 @@ class TheBrainV2 {
             if (claim) {
                 const cf = checkClaimFreshness(claim, resolver, semanticDiff);
                 const unverified = (cf.unverifiedFiles?.length ?? 0) > 0;
+                const trackedClaim = trackedClaimArtifactCount(claim);
                 return {
                     id,
-                    status: cf.fresh ? 'fresh' : unverified ? 'unverified' : 'stale',
+                    status: unverified ? 'unverified' : !cf.fresh ? 'stale' : trackedClaim === 0 ? 'untracked' : 'fresh',
+                    trackedArtifacts: trackedClaim,
                     ...(cf.staleFiles ? { staleFiles: cf.staleFiles } : {}),
                     ...(cf.unverifiedFiles ? { unverifiedFiles: cf.unverifiedFiles } : {}),
                     ...(cf.cosmeticChanges ? { cosmeticChanges: cf.cosmeticChanges } : {}),
@@ -1902,6 +2143,7 @@ class TheBrainV2 {
         let neverHit = 0;
         let downvoted = 0;
         let unscoped = 0;
+        let untracked = 0;
         let oldest = '';
         const bySource = {};
         const projects = new Set();
@@ -1914,6 +2156,8 @@ class TheBrainV2 {
                 unscoped++;
             else
                 projects.add(entry.projectId);
+            if (trackedArtifactCount(entry) === 0)
+                untracked++;
             const src = entrySource(entry);
             bySource[src] = (bySource[src] || 0) + 1;
             if (entry.timestamp && (!oldest || entry.timestamp < oldest))
@@ -1924,6 +2168,7 @@ class TheBrainV2 {
         base.bySource = bySource;
         base.projects = projects.size;
         base.unscopedEntries = unscoped;
+        base.untrackedEntries = untracked;
         base.tombstones = this.tombstones.size;
         if (oldest)
             base.oldestEntry = oldest;