sverklo 0.20.22 → 0.20.24

package/dist/src/indexer/indexer.js

@@ -166,6 +166,10 @@ export class Indexer {
             log(`[migration] data_version ${stored} → 10: clearing corrupted dependency graph (sv-p4-04 fix); next index will re-parse all files`);
             this.db.exec("DELETE FROM dependencies");
             this.db.exec("UPDATE files SET hash = '', last_modified = 0");
+            // Direct bulk SQL bypasses FileStore.upsert/delete/updatePagerank,
+            // so the in-memory getAll snapshot cache wouldn't auto-invalidate
+            // here. Explicit drop so the next getAll() reflects the migration.
+            this.fileStore.invalidateCache();
         }
         setDataVersion(this.db, CURRENT_DATA_VERSION);
     }

package/dist/src/indexer/indexer.js.map

@@ -1 +1 @@
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package/dist/src/indexer/watcher.js

@@ -22,6 +22,19 @@ export function startWatcher(indexer, rootPath) {
     // Debounce map: path -> timeout
     const pending = new Map();
     const DEBOUNCE_MS = 500;
+    // Serial reindex queue. Without this, a directory rename of N files
+    // fires N debounce timers ~simultaneously, each awaiting its own
+    // indexer.reindexFile() — N concurrent ONNX embedding calls hit the
+    // single embedder session. Architectural review 2026-05-13 (Tier 3.5
+    // / Backend B6) flagged the unbounded concurrency as exactly the
+    // backpressure gap. We serialize through a single Promise chain so
+    // ONNX sees one call at a time but no events are dropped.
+    let queueTail = Promise.resolve();
+    function enqueueReindex(work) {
+        const next = queueTail.then(work, work);
+        queueTail = next.catch(() => { });
+        return next;
+    }
     const watcher = watch(rootPath, {
         ignored: (path) => {
             const rel = relForward(rootPath, path);
@@ -52,9 +65,9 @@ export function startWatcher(indexer, rootPath) {
         const existing = pending.get("__config__");
         if (existing)
             clearTimeout(existing);
-        pending.set("__config__", setTimeout(async () => {
+        pending.set("__config__", setTimeout(() => {
             pending.delete("__config__");
-            await indexer.index();
+            enqueueReindex(() => indexer.index());
         }, DEBOUNCE_MS));
     }
     function handleChange(absolutePath) {
@@ -74,10 +87,10 @@ export function startWatcher(indexer, rootPath) {
         const existing = pending.get(rel);
         if (existing)
             clearTimeout(existing);
-        pending.set(rel, setTimeout(async () => {
+        pending.set(rel, setTimeout(() => {
             pending.delete(rel);
             log(`File changed: ${rel}`);
-            await indexer.reindexFile(rel, absolutePath, lang);
+            enqueueReindex(() => indexer.reindexFile(rel, absolutePath, lang));
         }, DEBOUNCE_MS));
     }
     watcher.on("add", handleChange);

package/dist/src/indexer/watcher.js.map

@@ -1 +1 @@
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package/dist/src/search/hybrid-search.js

@@ -128,9 +128,16 @@ async function rankCandidates(indexer, options) {
             }
         }
     }
-    // Add chunks from top PageRank files (structurally important), cap total candidates
+    // Add chunks from top PageRank files (structurally important), cap total candidates.
+    // Single fileStore.getAll() scan for both the top-20 PR slice AND the
+    // file lookup map (was called twice on every warm search call before
+    // the 2026-05-13 perf review — P4 in the Performance synthesis).
     const MAX_CANDIDATES = 500;
-    const topFiles = indexer.fileStore.getAll().slice(0, 20); // already sorted by pagerank DESC
+    const allFiles = indexer.fileStore.getAll(); // already sorted by pagerank DESC
+    const fileCache = new Map();
+    for (const f of allFiles)
+        fileCache.set(f.id, f);
+    const topFiles = allFiles.slice(0, 20);
     for (const f of topFiles) {
         if (candidateChunkIds.size >= MAX_CANDIDATES)
             break;
@@ -150,11 +157,6 @@ async function rankCandidates(indexer, options) {
     }
     vectorScores.sort((a, b) => b.score - a.score);
     const topVector = vectorScores.slice(0, 50);
-    // Build file cache for PageRank lookup
-    const fileCache = new Map();
-    for (const f of indexer.fileStore.getAll()) {
-        fileCache.set(f.id, f);
-    }
     // Reciprocal Rank Fusion
     const rrfScores = new Map();
     // Add FTS scores
@@ -169,10 +171,19 @@ async function rankCandidates(indexer, options) {
         const score = 1 / (RRF_K + rank + 1);
         rrfScores.set(chunkId, (rrfScores.get(chunkId) || 0) + score);
     }
+    // Batch-load candidate chunks in ONE SQLite query instead of N
+    // chunkStore.getById point reads. RRF candidate set is bounded by
+    // MAX_CANDIDATES (~500), well within SQLITE_MAX_VARIABLE_NUMBER.
+    // Perf review 2026-05-13 (P4) estimated 30-50ms warm-call win.
+    const candidateIds = Array.from(rrfScores.keys());
+    const chunksById = new Map();
+    for (const chunk of indexer.chunkStore.getByIds(candidateIds)) {
+        chunksById.set(chunk.id, chunk);
+    }
     // Collect candidates with full data
     const candidates = [];
     for (const [chunkId, rrfScore] of rrfScores) {
-        const chunk = indexer.chunkStore.getById(chunkId);
+        const chunk = chunksById.get(chunkId);
         if (!chunk)
             continue;
         const file = fileCache.get(chunk.file_id);

package/dist/src/search/hybrid-search.js.map

@@ -1 +1 @@
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package/dist/src/search/pagerank.js

@@ -1,6 +1,19 @@
 // PageRank implementation for file importance ranking.
 // Aider's key innovation: apply PageRank to the dependency graph
 // so that structurally important files (many importers) rank higher.
+//
+// Performance: this is a hot path on cold-start (runs once per index())
+// and on every reindexFile (file watcher). At 4000-file scale, the
+// arithmetic is fast but the data-layout was Map<Set> — each iteration
+// did O(edges) Map.get + Set.iteration, and the pointer-chasing
+// dominated over the math.
+//
+// Architectural review 2026-05-13 (Tier 2.4 / Perf P6) flagged this as
+// a structural data-layout fix. We now build a Compressed Sparse Row
+// (CSR) representation once: in-edges packed contiguously into an
+// Int32Array, indexed by per-node offset arrays. Iteration is
+// straight integer indexing into typed arrays — V8 hot-path
+// friendly, no object allocation per access.
 const DAMPING = 0.85;
 const ITERATIONS = 20;
 const CONVERGENCE_THRESHOLD = 0.0001;
@@ -8,57 +21,97 @@ export function computePageRank(fileIds, edges) {
     const n = fileIds.length;
     if (n === 0)
         return new Map();
-    // Build adjacency lists
-    const outLinks = new Map();
-    const inLinks = new Map();
-    for (const id of fileIds) {
-        outLinks.set(id, new Set());
-        inLinks.set(id, new Set());
+    // Map fileId → dense node index (0..n-1) so we can use typed arrays
+    // for everything downstream. Map.get is O(1) but allocates entries;
+    // we pay this once for setup, then it's pure integer math.
+    const idToIdx = new Map();
+    for (let i = 0; i < n; i++)
+        idToIdx.set(fileIds[i], i);
+    // Build CSR for IN-edges (we need "incomers" of each node during
+    // iteration) plus a per-node OUT-degree counter for the divide step.
+    const outDegree = new Int32Array(n);
+    // First pass: count in-edges per target and out-edges per source so
+    // we know the slice sizes.
+    const inDegree = new Int32Array(n);
+    // Pre-filter edges to those whose endpoints are in our index. Edges
+    // pointing to files we don't have (e.g. removed during a partial
+    // reindex) can't contribute.
+    const validEdges = [];
+    for (const e of edges) {
+        const srcIdx = idToIdx.get(e.source);
+        const tgtIdx = idToIdx.get(e.target);
+        if (srcIdx === undefined || tgtIdx === undefined)
+            continue;
+        validEdges.push({ srcIdx, tgtIdx });
+        outDegree[srcIdx]++;
+        inDegree[tgtIdx]++;
     }
-    for (const { source, target } of edges) {
-        outLinks.get(source)?.add(target);
-        inLinks.get(target)?.add(source);
+    // CSR offsets: inOffsets[i] = start index in inEdges array for
+    // node i's incomers. Last entry is total length (so slice from
+    // [inOffsets[i], inOffsets[i+1]) gives node i's incomers).
+    const inOffsets = new Int32Array(n + 1);
+    for (let i = 0; i < n; i++)
+        inOffsets[i + 1] = inOffsets[i] + inDegree[i];
+    // Pack in-edges contiguously: inEdges[k] = source node index of the
+    // k-th incomer (across all nodes, ordered by target).
+    const inEdges = new Int32Array(validEdges.length);
+    // Use a copy of inOffsets as a write cursor since we'll consume each
+    // slot in order.
+    const cursor = new Int32Array(n);
+    for (let i = 0; i < n; i++)
+        cursor[i] = inOffsets[i];
+    for (const { srcIdx, tgtIdx } of validEdges) {
+        inEdges[cursor[tgtIdx]++] = srcIdx;
     }
-    // Initialize ranks equally
-    let ranks = new Map();
+    // Two rank arrays we swap each iteration. Float64Array because IEEE-754
+    // arithmetic on millions of edges is cheaper on the typed-array path
+    // than boxed Number objects in Map values.
+    let ranks = new Float64Array(n);
+    let newRanks = new Float64Array(n);
     const initialRank = 1 / n;
-    for (const id of fileIds) {
-        ranks.set(id, initialRank);
-    }
-    // Iterate
+    for (let i = 0; i < n; i++)
+        ranks[i] = initialRank;
+    const teleport = (1 - DAMPING) / n;
     for (let iter = 0; iter < ITERATIONS; iter++) {
-        const newRanks = new Map();
         let maxDelta = 0;
-        for (const id of fileIds) {
+        for (let i = 0; i < n; i++) {
             let incomingRank = 0;
-            const incomers = inLinks.get(id);
-            if (incomers) {
-                for (const srcId of incomers) {
-                    const srcOutDegree = outLinks.get(srcId)?.size || 1;
-                    incomingRank += (ranks.get(srcId) || 0) / srcOutDegree;
-                }
+            const start = inOffsets[i];
+            const end = inOffsets[i + 1];
+            for (let k = start; k < end; k++) {
+                const srcIdx = inEdges[k];
+                const deg = outDegree[srcIdx] || 1;
+                incomingRank += ranks[srcIdx] / deg;
             }
-            const newRank = (1 - DAMPING) / n + DAMPING * incomingRank;
-            newRanks.set(id, newRank);
-            const delta = Math.abs(newRank - (ranks.get(id) || 0));
+            const r = teleport + DAMPING * incomingRank;
+            newRanks[i] = r;
+            const delta = r > ranks[i] ? r - ranks[i] : ranks[i] - r;
             if (delta > maxDelta)
                 maxDelta = delta;
         }
+        // Swap. Reuse the old `ranks` buffer as the next iteration's
+        // scratch — no allocation per iteration.
+        const tmp = ranks;
         ranks = newRanks;
+        newRanks = tmp;
         if (maxDelta < CONVERGENCE_THRESHOLD)
             break;
     }
     // Normalize to 0-1 range
     let maxRank = 0;
-    for (const r of ranks.values()) {
-        if (r > maxRank)
-            maxRank = r;
+    for (let i = 0; i < n; i++) {
+        if (ranks[i] > maxRank)
+            maxRank = ranks[i];
     }
+    const result = new Map();
     if (maxRank > 0) {
-        for (const [id, r] of ranks) {
-            ranks.set(id, r / maxRank);
-        }
+        for (let i = 0; i < n; i++)
+            result.set(fileIds[i], ranks[i] / maxRank);
+    }
+    else {
+        for (let i = 0; i < n; i++)
+            result.set(fileIds[i], ranks[i]);
     }
-    return ranks;
+    return result;
 }
 //# sourceMappingURL=pagerank.js.map

package/dist/src/search/pagerank.js.map

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package/dist/src/server/tools/overview.js

@@ -1,5 +1,6 @@
 import { formatOverview } from "../../search/token-budget.js";
 import { resolveBudget } from "../../utils/budget.js";
+import { isVendoredPath } from "../audit-analysis.js";
 export const overviewTool = {
     name: "sverklo_overview",
     description: "Get a structural map of the codebase. Shows the most important files and their key symbols ranked by dependency importance (PageRank). Use this FIRST when starting work on an unfamiliar codebase or directory.",
@@ -25,13 +26,33 @@ export const overviewTool = {
     },
 };
 export function handleOverview(indexer, args) {
-    const path = args.path;
+    // Normalize the path param: accept "src", "src/", or "./src". Drops
+    // trailing slash, strips leading "./". Without normalization, a user
+    // passing "src/" would match files where the prefix happens to
+    // include a slash but miss files starting at the bare directory
+    // name. Dogfood T4 fix per architectural review 2026-05-13.
+    const rawPath = args.path;
+    const path = rawPath
+        ? rawPath.replace(/^\.\/+/, "").replace(/\/+$/, "")
+        : undefined;
     const tokenBudget = resolveBudget(args, "overview", null, 3000);
     const files = indexer.fileStore.getAll(); // already sorted by pagerank DESC
     const entries = [];
     for (const file of files) {
-        if (path && !file.path.startsWith(path))
+        // Skip vendored / cached / generated paths so the overview reflects
+        // the user's own code, not third-party deps. Same exclusion as
+        // sverklo_audit (Dogfood T1 / T4 in the same review pass).
+        if (isVendoredPath(file.path))
             continue;
+        if (path) {
+            // Match "src" against "src/foo.ts" (prefix + boundary) but not
+            // against "src-utils/foo.ts" — require either exact match or
+            // a "/" right after the prefix.
+            if (file.path !== path &&
+                !file.path.startsWith(path + "/")) {
+                continue;
+            }
+        }
         const chunks = indexer.chunkStore.getByFile(file.id);
         entries.push({ file, chunks });
     }

package/dist/src/server/tools/overview.js.map

@@ -1 +1 @@
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+{"version":3,"file":"overview.js","sourceRoot":"","sources":["../../../../src/server/tools/overview.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,cAAc,EAAsB,MAAM,8BAA8B,CAAC;AAClF,OAAO,EAAE,aAAa,EAAE,MAAM,uBAAuB,CAAC;AACtD,OAAO,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAEtD,MAAM,CAAC,MAAM,YAAY,GAAG;IAC1B,IAAI,EAAE,kBAAkB;IACxB,WAAW,EACT,kNAAkN;IACpN,WAAW,EAAE;QACX,IAAI,EAAE,QAAiB;QACvB,UAAU,EAAE;YACV,IAAI,EAAE;gBACJ,IAAI,EAAE,QAAQ;gBACd,WAAW,EAAE,+CAA+C;aAC7D;YACD,YAAY,EAAE;gBACZ,IAAI,EAAE,QAAQ;gBACd,WAAW,EAAE,sCAAsC;aACpD;YACD,KAAK,EAAE;gBACL,IAAI,EAAE,QAAQ;gBACd,WAAW,EACT,6EAA6E;oBAC7E,kFAAkF;oBAClF,+EAA+E;oBAC/E,kEAAkE;aACrE;SACF;KACF;CACF,CAAC;AAEF,MAAM,UAAU,cAAc,CAC5B,OAAmB,EACnB,IAA6B;IAE7B,oEAAoE;IACpE,qEAAqE;IACrE,+DAA+D;IAC/D,gEAAgE;IAChE,4DAA4D;IAC5D,MAAM,OAAO,GAAG,IAAI,CAAC,IAA0B,CAAC;IAChD,MAAM,IAAI,GAAG,OAAO;QAClB,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC;QACnD,CAAC,CAAC,SAAS,CAAC;IACd,MAAM,WAAW,GAAG,aAAa,CAAC,IAAI,EAAE,UAAU,EAAE,IAAI,EAAE,IAAI,CAAC,CAAC;IAEhE,MAAM,KAAK,GAAG,OAAO,CAAC,SAAS,CAAC,MAAM,EAAE,CAAC,CAAC,kCAAkC;IAE5E,MAAM,OAAO,GAAoB,EAAE,CAAC;IACpC,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,oEAAoE;QACpE,+DAA+D;QAC/D,2DAA2D;QAC3D,IAAI,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC;YAAE,SAAS;QACxC,IAAI,IAAI,EAAE,CAAC;YACT,+DAA+D;YAC/D,6DAA6D;YAC7D,gCAAgC;YAChC,IACE,IAAI,CAAC,IAAI,KAAK,IAAI;gBAClB,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,IAAI,GAAG,GAAG,CAAC,EACjC,CAAC;gBACD,SAAS;YACX,CAAC;QACH,CAAC;QACD,MAAM,MAAM,GAAG,OAAO,CAAC,UAAU,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACrD,OAAO,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAC;IACjC,CAAC;IAED,MAAM,KAAK,GAAG,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IACrC,OAAO,cAAc,CAAC,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,KAAK,CAAC,CAAC;AAC3D,CAAC;AAED,SAAS,UAAU,CAAC,GAAY;IAC9B,MAAM,CAAC,GAAG,OAAO,GAAG,KAAK,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IACxD,IAAI,CAAC,IAAI,CAAC;QAAE,OAAO,CAAC,CAAC;IACrB,IAAI,CAAC,KAAK,CAAC;QAAE,OAAO,CAAC,CAAC;IACtB,IAAI,CAAC,IAAI,CAAC;QAAE,OAAO,CAAC,CAAC;IACrB,OAAO,CAAC,CAAC;AACX,CAAC"}

package/dist/src/storage/chunk-store.d.ts

@@ -16,6 +16,16 @@ export declare class ChunkStore {
         rank: number;
     })[];
     getById(id: number): CodeChunk | undefined;
+    /**
+     * Batched fetch by a set of chunk ids. Used by hybrid-search to enrich
+     * the RRF candidate set in one query instead of N point reads. The
+     * `WHERE id IN (...)` shape is built dynamically because better-sqlite3
+     * doesn't support array binding; we cap chunk-count at MAX_CANDIDATES
+     * (~500) upstream so the SQL stays well under SQLITE_MAX_VARIABLE_NUMBER.
+     * Returns chunks in arbitrary order — caller is responsible for the
+     * (chunkId → CodeChunk) mapping if ordering matters.
+     */
+    getByIds(ids: number[]): CodeChunk[];
     getByName(namePattern: string, limit?: number): CodeChunk[];
     /**
      * Same shape as getByName, but JOINs in the containing file's path and

package/dist/src/storage/chunk-store.js

@@ -57,6 +57,23 @@ export class ChunkStore {
     getById(id) {
         return this.getByIdStmt.get(id);
     }
+    /**
+     * Batched fetch by a set of chunk ids. Used by hybrid-search to enrich
+     * the RRF candidate set in one query instead of N point reads. The
+     * `WHERE id IN (...)` shape is built dynamically because better-sqlite3
+     * doesn't support array binding; we cap chunk-count at MAX_CANDIDATES
+     * (~500) upstream so the SQL stays well under SQLITE_MAX_VARIABLE_NUMBER.
+     * Returns chunks in arbitrary order — caller is responsible for the
+     * (chunkId → CodeChunk) mapping if ordering matters.
+     */
+    getByIds(ids) {
+        if (ids.length === 0)
+            return [];
+        const placeholders = ids.map(() => "?").join(",");
+        return this.db
+            .prepare(`SELECT * FROM chunks WHERE id IN (${placeholders})`)
+            .all(...ids);
+    }
     getByName(namePattern, limit = 20) {
         return this.getByNameStmt.all(`%${namePattern}%`, limit);
     }

package/dist/src/storage/chunk-store.js.map

@@ -1 +1 @@
-{"version":3,"file":"chunk-store.js","sourceRoot":"","sources":["../../../src/storage/chunk-store.ts"],"names":[],"mappings":"AAGA,MAAM,OAAO,UAAU;IAQD;IAPZ,UAAU,CAAqB;IAC/B,aAAa,CAAqB;IAClC,gBAAgB,CAAqB;IACrC,aAAa,CAAqB;IAClC,WAAW,CAAqB;IAChC,aAAa,CAAqB;IAE1C,YAAoB,EAAqB;QAArB,OAAE,GAAF,EAAE,CAAmB;QACvC,IAAI,CAAC,UAAU,GAAG,EAAE,CAAC,OAAO,CAAC;;;KAG5B,CAAC,CAAC;QACH,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,OAAO,CAC7B,4DAA4D,CAC7D,CAAC;QACF,IAAI,CAAC,gBAAgB,GAAG,EAAE,CAAC,OAAO,CAAC,sCAAsC,CAAC,CAAC;QAC3E,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,OAAO,CAAC;;;;;;;KAO/B,CAAC,CAAC;QACH,IAAI,CAAC,WAAW,GAAG,EAAE,CAAC,OAAO,CAAC,mCAAmC,CAAC,CAAC;QACnE,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,OAAO,CAAC;;KAE/B,CAAC,CAAC;IACL,CAAC;IAED,MAAM,CACJ,MAAc,EACd,IAAe,EACf,IAAmB,EACnB,SAAwB,EACxB,SAAiB,EACjB,OAAe,EACf,OAAe,EACf,WAA0B,EAC1B,UAAkB;QAElB,MAAM,MAAM,GAAG,IAAI,CAAC,UAAU,CAAC,GAAG,CAChC,MAAM,EACN,IAAI,EACJ,IAAI,EACJ,SAAS,EACT,SAAS,EACT,OAAO,EACP,OAAO,EACP,WAAW,EACX,UAAU,CACX,CAAC;QACF,OAAO,MAAM,CAAC,MAAM,CAAC,eAAe,CAAC,CAAC;IACxC,CAAC;IAED,SAAS,CAAC,MAAc;QACtB,OAAO,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,MAAM,CAAgB,CAAC;IACvD,CAAC;IAED,YAAY,CAAC,MAAc;QACzB,IAAI,CAAC,gBAAgB,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IACpC,CAAC;IAED,SAAS,CAAC,KAAa,EAAE,QAAgB,EAAE;QACzC,IAAI,CAAC;YACH,oDAAoD;YACpD,MAAM,SAAS,GAAG,KAAK;iBACpB,OAAO,CAAC,wBAAwB,EAAE,GAAG,CAAC;iBACtC,KAAK,CAAC,KAAK,CAAC;iBACZ,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC;iBAC3B,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC;iBACpB,IAAI,CAAC,MAAM,CAAC,CAAC;YAChB,IAAI,CAAC,SAAS;gBAAE,OAAO,EAAE,CAAC;YAC1B,OAAO,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,SAAS,EAAE,KAAK,CAE1C,CAAC;QACP,CAAC;QAAC,MAAM,CAAC;YACP,OAAO,EAAE,CAAC;QACZ,CAAC;IACH,CAAC;IAED,OAAO,CAAC,EAAU;QAChB,OAAO,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,CAA0B,CAAC;IAC3D,CAAC;IAED,SAAS,CAAC,WAAmB,EAAE,QAAgB,EAAE;QAC/C,OAAO,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,IAAI,WAAW,GAAG,EAAE,KAAK,CAAgB,CAAC;IAC1E,CAAC;IAED;;;;;;OAMG;IACH,iBAAiB,CACf,WAAmB,EACnB,QAAgB,EAAE;QAElB,iEAAiE;QACjE,8DAA8D;QAC9D,2DAA2D;QAC3D,iEAAiE;QACjE,8DAA8D;QAC9D,sCAAsC;QACtC,OAAO,IAAI,CAAC,EAAE;aACX,OAAO,CACN;;;;;;;;;iBASS,CACV;aACA,GAAG,CAAC,WAAW,EAAE,GAAG,WAAW,GAAG,EAAE,IAAI,WAAW,GAAG,EAAE,KAAK,CAI5D,CAAC;IACP,CAAC;IAED,KAAK;QACH,OACE,IAAI,CAAC,EAAE,CAAC,OAAO,CAAC,kCAAkC,CAAC,CAAC,GAAG,EACxD,CAAC,CAAC,CAAC;IACN,CAAC;IAED,mDAAmD;IACnD,aAAa,CAAC,OAAe,EAAE,OAAsB;QACnD,IAAI,CAAC,EAAE,CAAC,OAAO,CAAC,4CAA4C,CAAC,CAAC,GAAG,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;IACtF,CAAC;IAED;iCAC6B;IAC7B,UAAU,CAAC,OAAe;QACxB,MAAM,GAAG,GAAG,IAAI,CAAC,EAAE;aAChB,OAAO,CAAC,yCAAyC,CAAC;aAClD,GAAG,CAAC,OAAO,CAA2C,CAAC;QAC1D,OAAO,GAAG,EAAE,OAAO,IAAI,IAAI,CAAC;IAC9B,CAAC;IAED,cAAc;QACZ,OAAO,IAAI,CAAC,EAAE;aACX,OAAO,CACN;;gDAEwC,CACzC;aACA,GAAG,EAA4D,CAAC;IACrE,CAAC;CACF"}
+{"version":3,"file":"chunk-store.js","sourceRoot":"","sources":["../../../src/storage/chunk-store.ts"],"names":[],"mappings":"AAGA,MAAM,OAAO,UAAU;IAQD;IAPZ,UAAU,CAAqB;IAC/B,aAAa,CAAqB;IAClC,gBAAgB,CAAqB;IACrC,aAAa,CAAqB;IAClC,WAAW,CAAqB;IAChC,aAAa,CAAqB;IAE1C,YAAoB,EAAqB;QAArB,OAAE,GAAF,EAAE,CAAmB;QACvC,IAAI,CAAC,UAAU,GAAG,EAAE,CAAC,OAAO,CAAC;;;KAG5B,CAAC,CAAC;QACH,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,OAAO,CAC7B,4DAA4D,CAC7D,CAAC;QACF,IAAI,CAAC,gBAAgB,GAAG,EAAE,CAAC,OAAO,CAAC,sCAAsC,CAAC,CAAC;QAC3E,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,OAAO,CAAC;;;;;;;KAO/B,CAAC,CAAC;QACH,IAAI,CAAC,WAAW,GAAG,EAAE,CAAC,OAAO,CAAC,mCAAmC,CAAC,CAAC;QACnE,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,OAAO,CAAC;;KAE/B,CAAC,CAAC;IACL,CAAC;IAED,MAAM,CACJ,MAAc,EACd,IAAe,EACf,IAAmB,EACnB,SAAwB,EACxB,SAAiB,EACjB,OAAe,EACf,OAAe,EACf,WAA0B,EAC1B,UAAkB;QAElB,MAAM,MAAM,GAAG,IAAI,CAAC,UAAU,CAAC,GAAG,CAChC,MAAM,EACN,IAAI,EACJ,IAAI,EACJ,SAAS,EACT,SAAS,EACT,OAAO,EACP,OAAO,EACP,WAAW,EACX,UAAU,CACX,CAAC;QACF,OAAO,MAAM,CAAC,MAAM,CAAC,eAAe,CAAC,CAAC;IACxC,CAAC;IAED,SAAS,CAAC,MAAc;QACtB,OAAO,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,MAAM,CAAgB,CAAC;IACvD,CAAC;IAED,YAAY,CAAC,MAAc;QACzB,IAAI,CAAC,gBAAgB,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IACpC,CAAC;IAED,SAAS,CAAC,KAAa,EAAE,QAAgB,EAAE;QACzC,IAAI,CAAC;YACH,oDAAoD;YACpD,MAAM,SAAS,GAAG,KAAK;iBACpB,OAAO,CAAC,wBAAwB,EAAE,GAAG,CAAC;iBACtC,KAAK,CAAC,KAAK,CAAC;iBACZ,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC;iBAC3B,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC;iBACpB,IAAI,CAAC,MAAM,CAAC,CAAC;YAChB,IAAI,CAAC,SAAS;gBAAE,OAAO,EAAE,CAAC;YAC1B,OAAO,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,SAAS,EAAE,KAAK,CAE1C,CAAC;QACP,CAAC;QAAC,MAAM,CAAC;YACP,OAAO,EAAE,CAAC;QACZ,CAAC;IACH,CAAC;IAED,OAAO,CAAC,EAAU;QAChB,OAAO,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,CAA0B,CAAC;IAC3D,CAAC;IAED;;;;;;;;OAQG;IACH,QAAQ,CAAC,GAAa;QACpB,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC;YAAE,OAAO,EAAE,CAAC;QAChC,MAAM,YAAY,GAAG,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QAClD,OAAO,IAAI,CAAC,EAAE;aACX,OAAO,CAAC,qCAAqC,YAAY,GAAG,CAAC;aAC7D,GAAG,CAAC,GAAG,GAAG,CAAgB,CAAC;IAChC,CAAC;IAED,SAAS,CAAC,WAAmB,EAAE,QAAgB,EAAE;QAC/C,OAAO,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,IAAI,WAAW,GAAG,EAAE,KAAK,CAAgB,CAAC;IAC1E,CAAC;IAED;;;;;;OAMG;IACH,iBAAiB,CACf,WAAmB,EACnB,QAAgB,EAAE;QAElB,iEAAiE;QACjE,8DAA8D;QAC9D,2DAA2D;QAC3D,iEAAiE;QACjE,8DAA8D;QAC9D,sCAAsC;QACtC,OAAO,IAAI,CAAC,EAAE;aACX,OAAO,CACN;;;;;;;;;iBASS,CACV;aACA,GAAG,CAAC,WAAW,EAAE,GAAG,WAAW,GAAG,EAAE,IAAI,WAAW,GAAG,EAAE,KAAK,CAI5D,CAAC;IACP,CAAC;IAED,KAAK;QACH,OACE,IAAI,CAAC,EAAE,CAAC,OAAO,CAAC,kCAAkC,CAAC,CAAC,GAAG,EACxD,CAAC,CAAC,CAAC;IACN,CAAC;IAED,mDAAmD;IACnD,aAAa,CAAC,OAAe,EAAE,OAAsB;QACnD,IAAI,CAAC,EAAE,CAAC,OAAO,CAAC,4CAA4C,CAAC,CAAC,GAAG,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;IACtF,CAAC;IAED;iCAC6B;IAC7B,UAAU,CAAC,OAAe;QACxB,MAAM,GAAG,GAAG,IAAI,CAAC,EAAE;aAChB,OAAO,CAAC,yCAAyC,CAAC;aAClD,GAAG,CAAC,OAAO,CAA2C,CAAC;QAC1D,OAAO,GAAG,EAAE,OAAO,IAAI,IAAI,CAAC;IAC9B,CAAC;IAED,cAAc;QACZ,OAAO,IAAI,CAAC,EAAE;aACX,OAAO,CACN;;gDAEwC,CACzC;aACA,GAAG,EAA4D,CAAC;IACrE,CAAC;CACF"}

package/dist/src/storage/file-store.d.ts

@@ -8,12 +8,19 @@ export declare class FileStore {
     private deleteStmt;
     private updatePagerankStmt;
     private getLanguagesStmt;
+    private cachedAll;
     constructor(db: Database.Database);
     upsert(path: string, language: string | null, hash: string, lastModified: number, sizeBytes: number): number;
     getByPath(path: string): FileRecord | undefined;
     getAll(): FileRecord[];
     delete(path: string): void;
     updatePagerank(id: number, score: number): void;
+    /**
+     * Drop the snapshot. Call after bulk operations (transactions,
+     * migrations) that mutate the files table without going through the
+     * upsert/delete/updatePagerank methods. Cheap no-op if already null.
+     */
+    invalidateCache(): void;
     getLanguages(): string[];
     count(): number;
 }

package/dist/src/storage/file-store.js

@@ -6,6 +6,17 @@ export class FileStore {
     deleteStmt;
     updatePagerankStmt;
     getLanguagesStmt;
+    // In-memory snapshot of every getAll() result. The file set turns over
+    // rarely (only on indexer writes), but is read 20+ times per tool
+    // invocation across audit, clusters, wiki, investigate, dependencies,
+    // and find-references. Without this cache, each handler re-scanned the
+    // files table from SQLite — that's full-table reads stacking up on
+    // every warm MCP call.
+    //
+    // Architectural review 2026-05-13 (Perf P7) measured 10-30ms per
+    // affected call. Invalidation is internal: upsert / delete /
+    // updatePagerank null the cache, so the next read repopulates.
+    cachedAll = null;
     constructor(db) {
         this.db = db;
         // INSERT OR REPLACE used to be the implementation here, and it had a
@@ -40,19 +51,33 @@ export class FileStore {
     }
     upsert(path, language, hash, lastModified, sizeBytes) {
         const row = this.insertStmt.get(path, language, hash, lastModified, sizeBytes, Date.now());
+        this.cachedAll = null;
         return row.id;
     }
     getByPath(path) {
         return this.getByPathStmt.get(path);
     }
     getAll() {
-        return this.getAllStmt.all();
+        if (this.cachedAll !== null)
+            return this.cachedAll;
+        this.cachedAll = this.getAllStmt.all();
+        return this.cachedAll;
     }
     delete(path) {
         this.deleteStmt.run(path);
+        this.cachedAll = null;
     }
     updatePagerank(id, score) {
         this.updatePagerankStmt.run(score, id);
+        this.cachedAll = null;
+    }
+    /**
+     * Drop the snapshot. Call after bulk operations (transactions,
+     * migrations) that mutate the files table without going through the
+     * upsert/delete/updatePagerank methods. Cheap no-op if already null.
+     */
+    invalidateCache() {
+        this.cachedAll = null;
     }
     getLanguages() {
         return this.getLanguagesStmt.all().map((r) => r.language);

package/dist/src/storage/file-store.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "sverklo",
   "mcpName": "io.github.sverklo/sverklo",
-  "version": "0.20.22",
+  "version": "0.20.24",
   "description": "Local-first code intelligence — MCP server for Claude Code, Cursor, Windsurf, Zed. Symbol graph, blast-radius, git-pinned memory. 43× fewer tokens than naive grep on the public bench. MIT, zero-config.",
   "type": "module",
   "bin": {