codesift-mcp 0.1.0 → 0.2.1

package/dist/storage/embedding-store.js

@@ -1,5 +1,5 @@
-import { readFile, writeFile, rename, mkdir, unlink } from "node:fs/promises";
-import { dirname } from "node:path";
+import { readFile } from "node:fs/promises";
+import { atomicWriteFile } from "./_shared.js";
 /**
  * Get the embedding file path from an index path.
  * {hash}.index.json → {hash}.embeddings.ndjson
@@ -45,26 +45,42 @@ export async function loadEmbeddings(embeddingPath) {
     return embeddings;
 }
 /**
- * Save all embeddings atomically to an ndjson file.
+ * Save all embeddings to an ndjson file using streaming writes.
+ * Avoids building a single huge string (30K+ symbols × 1536 floats = >300MB).
  */
 export async function saveEmbeddings(embeddingPath, embeddings) {
-    const dir = dirname(embeddingPath);
-    await mkdir(dir, { recursive: true });
-    const lines = [];
-    for (const [id, vec] of embeddings) {
-        lines.push(JSON.stringify({ id, vec: Array.from(vec) }));
-    }
     const tmpPath = `${embeddingPath}.tmp.${Date.now()}`;
-    const data = lines.join("\n") + "\n";
+    const { createWriteStream } = await import("node:fs");
+    const stream = createWriteStream(tmpPath, { encoding: "utf-8" });
+    // Register error listener immediately to prevent unhandled error crash
+    let streamError = null;
+    stream.on("error", (err) => { streamError = err; });
     try {
-        await writeFile(tmpPath, data, "utf-8");
+        for (const [id, vec] of embeddings) {
+            if (streamError)
+                throw streamError;
+            const line = JSON.stringify({ id, vec: Array.from(vec) }) + "\n";
+            const canContinue = stream.write(line);
+            if (!canContinue) {
+                await new Promise((resolve) => stream.once("drain", resolve));
+            }
+        }
+        if (streamError)
+            throw streamError;
+        await new Promise((resolve, reject) => {
+            stream.end(() => streamError ? reject(streamError) : resolve());
+        });
+        // Atomic rename
+        const { rename } = await import("node:fs/promises");
         await rename(tmpPath, embeddingPath);
     }
     catch (err) {
+        // Clean up temp file on error
         try {
+            const { unlink } = await import("node:fs/promises");
             await unlink(tmpPath);
         }
-        catch { /* cleanup best-effort */ }
+        catch { /* ignore */ }
         throw err;
     }
 }
@@ -72,21 +88,8 @@ export async function saveEmbeddings(embeddingPath, embeddings) {
  * Save embedding metadata atomically.
  */
 export async function saveEmbeddingMeta(metaPath, meta) {
-    const dir = dirname(metaPath);
-    await mkdir(dir, { recursive: true });
-    const tmpPath = `${metaPath}.tmp.${Date.now()}`;
     const data = JSON.stringify(meta);
-    try {
-        await writeFile(tmpPath, data, "utf-8");
-        await rename(tmpPath, metaPath);
-    }
-    catch (err) {
-        try {
-            await unlink(tmpPath);
-        }
-        catch { /* cleanup best-effort */ }
-        throw err;
-    }
+    await atomicWriteFile(metaPath, data);
 }
 /**
  * Load embedding metadata.
@@ -107,24 +110,41 @@ export async function loadEmbeddingMeta(metaPath) {
         return null;
     }
 }
+/** Simple hash for content-change detection (FNV-1a 32-bit). */
+function contentHash(text) {
+    let h = 0x811c9dc5;
+    for (let i = 0; i < text.length; i++) {
+        h ^= text.charCodeAt(i);
+        h = Math.imul(h, 0x01000193);
+    }
+    return h >>> 0;
+}
+/** Track content hashes so we re-embed when symbol content changes. */
+const embeddingContentHashes = new Map();
 /**
  * Batch-embed symbols using the given provider, appending to existing embeddings.
- * Only embeds symbols that don't already have an embedding.
+ * Skips symbols whose ID exists AND content hash hasn't changed.
+ * Re-embeds symbols whose content changed even if ID is the same.
  *
  * @param symbolTexts - Map of symbolId → text to embed
  * @param existing - Existing embeddings to skip
  * @param embedFn - The provider's embed function
  * @param batchSize - How many texts per API call
+ * @param cacheKey - Optional key to track content hashes across calls
  * @returns Map of symbolId → Float32Array (existing + new)
  */
-export async function batchEmbed(symbolTexts, existing, embedFn, batchSize) {
+export async function batchEmbed(symbolTexts, existing, embedFn, batchSize, cacheKey) {
     const result = new Map(existing);
-    // Find symbols that need embedding
+    const hashes = cacheKey ? (embeddingContentHashes.get(cacheKey) ?? new Map()) : new Map();
+    // Find symbols that need embedding (new or content changed)
     const toEmbed = [];
     for (const [id, text] of symbolTexts) {
-        if (!existing.has(id)) {
+        const hash = contentHash(text);
+        const needsEmbed = !existing.has(id) || (cacheKey !== undefined && hashes.get(id) !== hash);
+        if (needsEmbed) {
             toEmbed.push({ id, text });
         }
+        hashes.set(id, hash);
     }
     // Process in batches (only symbols that need embedding)
     for (let i = 0; i < toEmbed.length; i += batchSize) {
@@ -143,6 +163,10 @@ export async function batchEmbed(symbolTexts, existing, embedFn, batchSize) {
     const stale = [...result.keys()].filter((id) => !symbolTexts.has(id));
     for (const id of stale) {
         result.delete(id);
+        hashes.delete(id);
+    }
+    if (cacheKey) {
+        embeddingContentHashes.set(cacheKey, hashes);
     }
     return result;
 }

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package/dist/storage/graph-store.d.ts

@@ -0,0 +1,48 @@
+/**
+ * Persistent knowledge graph — caches symbol relationships (import edges,
+ * call chains, type usage) across sessions to avoid expensive recomputation.
+ *
+ * Stored as JSON alongside the index file. Invalidated when the index changes
+ * (via content hash comparison).
+ */
+export interface GraphEdge {
+    from: string;
+    to: string;
+    kind: "imports" | "calls" | "uses_type" | "extends" | "implements";
+}
+export interface PersistentGraph {
+    /** Hash of the index content — used to detect staleness */
+    index_hash: string;
+    /** Timestamp of last computation */
+    computed_at: number;
+    /** Import edges between files */
+    edges: GraphEdge[];
+    /** Module-level stats */
+    modules: Array<{
+        path: string;
+        symbol_count: number;
+        in_degree: number;
+        out_degree: number;
+    }>;
+    /** Detected circular dependencies */
+    circular_deps: string[][];
+}
+/**
+ * Get the graph store path from an index path.
+ * {hash}.index.json → {hash}.graph.json
+ */
+export declare function getGraphPath(indexPath: string): string;
+/** Compute a hash from index file paths + symbol counts (cheap staleness check). */
+export declare function computeIndexHash(files: Array<{
+    path: string;
+    symbol_count: number;
+}>): string;
+/**
+ * Load a persisted graph. Returns null if not found, corrupted, or stale.
+ */
+export declare function loadGraph(graphPath: string, currentIndexHash: string): Promise<PersistentGraph | null>;
+/**
+ * Save a computed graph to disk.
+ */
+export declare function saveGraph(graphPath: string, graph: PersistentGraph): Promise<void>;
+//# sourceMappingURL=graph-store.d.ts.map

package/dist/storage/graph-store.d.ts.map

@@ -0,0 +1 @@
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package/dist/storage/graph-store.js

@@ -0,0 +1,52 @@
+import { readFile } from "node:fs/promises";
+import { atomicWriteFile } from "./_shared.js";
+/**
+ * Get the graph store path from an index path.
+ * {hash}.index.json → {hash}.graph.json
+ */
+export function getGraphPath(indexPath) {
+    return indexPath.replace(/\.index\.json$/, ".graph.json");
+}
+/** Simple FNV-1a hash for content-change detection. */
+function fnv1a(text) {
+    let h = 0x811c9dc5;
+    for (let i = 0; i < text.length; i++) {
+        h ^= text.charCodeAt(i);
+        h = Math.imul(h, 0x01000193);
+    }
+    return (h >>> 0).toString(16);
+}
+/** Compute a hash from index file paths + symbol counts (cheap staleness check). */
+export function computeIndexHash(files) {
+    const fingerprint = files.map((f) => `${f.path}:${f.symbol_count}`).join("\n");
+    return fnv1a(fingerprint);
+}
+/**
+ * Load a persisted graph. Returns null if not found, corrupted, or stale.
+ */
+export async function loadGraph(graphPath, currentIndexHash) {
+    try {
+        const raw = await readFile(graphPath, "utf-8");
+        const parsed = JSON.parse(raw);
+        if (typeof parsed === "object" && parsed !== null &&
+            typeof parsed["index_hash"] === "string" &&
+            Array.isArray(parsed["edges"])) {
+            const graph = parsed;
+            // Stale check: index changed since last computation
+            if (graph.index_hash !== currentIndexHash)
+                return null;
+            return graph;
+        }
+        return null;
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * Save a computed graph to disk.
+ */
+export async function saveGraph(graphPath, graph) {
+    await atomicWriteFile(graphPath, JSON.stringify(graph));
+}
+//# sourceMappingURL=graph-store.js.map

package/dist/storage/graph-store.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"graph-store.js","sourceRoot":"","sources":["../../src/storage/graph-store.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAC5C,OAAO,EAAE,eAAe,EAAE,MAAM,cAAc,CAAC;AA6B/C;;;GAGG;AACH,MAAM,UAAU,YAAY,CAAC,SAAiB;IAC5C,OAAO,SAAS,CAAC,OAAO,CAAC,gBAAgB,EAAE,aAAa,CAAC,CAAC;AAC5D,CAAC;AAED,uDAAuD;AACvD,SAAS,KAAK,CAAC,IAAY;IACzB,IAAI,CAAC,GAAG,UAAU,CAAC;IACnB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACrC,CAAC,IAAI,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC;QACxB,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,UAAU,CAAC,CAAC;IAC/B,CAAC;IACD,OAAO,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC;AAChC,CAAC;AAED,oFAAoF;AACpF,MAAM,UAAU,gBAAgB,CAAC,KAAoD;IACnF,MAAM,WAAW,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,YAAY,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAC/E,OAAO,KAAK,CAAC,WAAW,CAAC,CAAC;AAC5B,CAAC;AAED;;GAEG;AACH,MAAM,CAAC,KAAK,UAAU,SAAS,CAC7B,SAAiB,EACjB,gBAAwB;IAExB,IAAI,CAAC;QACH,MAAM,GAAG,GAAG,MAAM,QAAQ,CAAC,SAAS,EAAE,OAAO,CAAC,CAAC;QAC/C,MAAM,MAAM,GAAY,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;QAExC,IACE,OAAO,MAAM,KAAK,QAAQ,IAAI,MAAM,KAAK,IAAI;YAC7C,OAAQ,MAAkC,CAAC,YAAY,CAAC,KAAK,QAAQ;YACrE,KAAK,CAAC,OAAO,CAAE,MAAkC,CAAC,OAAO,CAAC,CAAC,EAC3D,CAAC;YACD,MAAM,KAAK,GAAG,MAAyB,CAAC;YACxC,oDAAoD;YACpD,IAAI,KAAK,CAAC,UAAU,KAAK,gBAAgB;gBAAE,OAAO,IAAI,CAAC;YACvD,OAAO,KAAK,CAAC;QACf,CAAC;QACD,OAAO,IAAI,CAAC;IACd,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC;AAED;;GAEG;AACH,MAAM,CAAC,KAAK,UAAU,SAAS,CAC7B,SAAiB,EACjB,KAAsB;IAEtB,MAAM,eAAe,CAAC,SAAS,EAAE,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC;AAC1D,CAAC"}

package/dist/storage/index-store.d.ts

@@ -15,6 +15,11 @@ export declare function loadIndex(indexPath: string): Promise<CodeIndex | null>;
  * Serialized per indexPath to prevent read-modify-write races.
  */
 export declare function saveIncremental(indexPath: string, updatedFile: string, newSymbols: CodeSymbol[], fileEntry?: FileEntry): Promise<void>;
+/**
+ * Remove all symbols and the file entry for a deleted file.
+ * Serialized per indexPath to prevent read-modify-write races.
+ */
+export declare function removeFileFromIndex(indexPath: string, deletedFile: string): Promise<void>;
 /**
  * Derive a deterministic index file path from a repo root.
  * Uses a truncated SHA-256 hash of the root path.

package/dist/storage/index-store.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index-store.d.ts","sourceRoot":"","sources":["../../src/storage/index-store.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,SAAS,EAAE,MAAM,aAAa,CAAC;AAKpE;;;GAGG;AACH,wBAAsB,SAAS,CAC7B,SAAS,EAAE,MAAM,EACjB,KAAK,EAAE,SAAS,GACf,OAAO,CAAC,IAAI,CAAC,CAcf;AAED;;;GAGG;AACH,wBAAsB,SAAS,CAC7B,SAAS,EAAE,MAAM,GAChB,OAAO,CAAC,SAAS,GAAG,IAAI,CAAC,CAa3B;AAED;;;;GAIG;AACH,wBAAsB,eAAe,CACnC,SAAS,EAAE,MAAM,EACjB,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,UAAU,EAAE,EACxB,SAAS,CAAC,EAAE,SAAS,GACpB,OAAO,CAAC,IAAI,CAAC,CAgCf;AAED;;;GAGG;AACH,wBAAgB,YAAY,CAAC,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,MAAM,CAOtE"}
+{"version":3,"file":"index-store.d.ts","sourceRoot":"","sources":["../../src/storage/index-store.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,SAAS,EAAE,MAAM,aAAa,CAAC;AAMpE;;;GAGG;AACH,wBAAsB,SAAS,CAC7B,SAAS,EAAE,MAAM,EACjB,KAAK,EAAE,SAAS,GACf,OAAO,CAAC,IAAI,CAAC,CAGf;AAED;;;GAGG;AACH,wBAAsB,SAAS,CAC7B,SAAS,EAAE,MAAM,GAChB,OAAO,CAAC,SAAS,GAAG,IAAI,CAAC,CAa3B;AAED;;;;GAIG;AACH,wBAAsB,eAAe,CACnC,SAAS,EAAE,MAAM,EACjB,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,UAAU,EAAE,EACxB,SAAS,CAAC,EAAE,SAAS,GACpB,OAAO,CAAC,IAAI,CAAC,CAgCf;AAED;;;GAGG;AACH,wBAAsB,mBAAmB,CACvC,SAAS,EAAE,MAAM,EACjB,WAAW,EAAE,MAAM,GAClB,OAAO,CAAC,IAAI,CAAC,CAsBf;AAED;;;GAGG;AACH,wBAAgB,YAAY,CAAC,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,MAAM,CAOtE"}

package/dist/storage/index-store.js

@@ -1,6 +1,7 @@
-import { readFile, writeFile, rename, mkdir, unlink } from "node:fs/promises";
-import { join, dirname } from "node:path";
+import { readFile } from "node:fs/promises";
+import { join } from "node:path";
 import { createHash } from "node:crypto";
+import { atomicWriteFile } from "./_shared.js";
 /** Serialize concurrent writes to the same index path. */
 const writeLocks = new Map();
 /**
@@ -8,21 +9,8 @@ const writeLocks = new Map();
  * Writes to a temp file first, then renames to prevent partial reads.
  */
 export async function saveIndex(indexPath, index) {
-    const dir = dirname(indexPath);
-    await mkdir(dir, { recursive: true });
-    const tmpPath = `${indexPath}.tmp.${Date.now()}.json`;
     const data = JSON.stringify(index);
-    try {
-        await writeFile(tmpPath, data, "utf-8");
-        await rename(tmpPath, indexPath);
-    }
-    catch (err) {
-        try {
-            await unlink(tmpPath);
-        }
-        catch { /* cleanup best-effort */ }
-        throw err;
-    }
+    await atomicWriteFile(indexPath, data);
 }
 /**
  * Load a code index from disk.
@@ -71,6 +59,30 @@ export async function saveIncremental(indexPath, updatedFile, newSymbols, fileEn
     writeLocks.set(indexPath, next.catch(() => { }));
     return next;
 }
+/**
+ * Remove all symbols and the file entry for a deleted file.
+ * Serialized per indexPath to prevent read-modify-write races.
+ */
+export async function removeFileFromIndex(indexPath, deletedFile) {
+    const prev = writeLocks.get(indexPath) ?? Promise.resolve();
+    const next = prev.then(async () => {
+        const existing = await loadIndex(indexPath);
+        if (!existing)
+            return;
+        const hadSymbols = existing.symbols.some((s) => s.file === deletedFile);
+        const hadFile = existing.files.some((f) => f.path === deletedFile);
+        if (!hadSymbols && !hadFile)
+            return;
+        existing.symbols = existing.symbols.filter((s) => s.file !== deletedFile);
+        existing.symbol_count = existing.symbols.length;
+        existing.files = existing.files.filter((f) => f.path !== deletedFile);
+        existing.file_count = existing.files.length;
+        existing.updated_at = Date.now();
+        await saveIndex(indexPath, existing);
+    });
+    writeLocks.set(indexPath, next.catch(() => { }));
+    return next;
+}
 /**
  * Derive a deterministic index file path from a repo root.
  * Uses a truncated SHA-256 hash of the root path.

package/dist/storage/index-store.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index-store.js","sourceRoot":"","sources":["../../src/storage/index-store.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAC5C,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AACjC,OAAO,EAAE,UAAU,EAAE,MAAM,aAAa,CAAC;AAEzC,OAAO,EAAE,eAAe,EAAE,MAAM,cAAc,CAAC;AAE/C,0DAA0D;AAC1D,MAAM,UAAU,GAAG,IAAI,GAAG,EAAyB,CAAC;AAEpD;;;GAGG;AACH,MAAM,CAAC,KAAK,UAAU,SAAS,CAC7B,SAAiB,EACjB,KAAgB;IAEhB,MAAM,IAAI,GAAG,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC;IACnC,MAAM,eAAe,CAAC,SAAS,EAAE,IAAI,CAAC,CAAC;AACzC,CAAC;AAED;;;GAGG;AACH,MAAM,CAAC,KAAK,UAAU,SAAS,CAC7B,SAAiB;IAEjB,IAAI,CAAC;QACH,MAAM,GAAG,GAAG,MAAM,QAAQ,CAAC,SAAS,EAAE,OAAO,CAAC,CAAC;QAC/C,MAAM,MAAM,GAAY,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;QAExC,IAAI,CAAC,YAAY,CAAC,MAAM,CAAC,EAAE,CAAC;YAC1B,OAAO,IAAI,CAAC;QACd,CAAC;QAED,OAAO,MAAM,CAAC;IAChB,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC;AAED;;;;GAIG;AACH,MAAM,CAAC,KAAK,UAAU,eAAe,CACnC,SAAiB,EACjB,WAAmB,EACnB,UAAwB,EACxB,SAAqB;IAErB,MAAM,IAAI,GAAG,UAAU,CAAC,GAAG,CAAC,SAAS,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,CAAC;IAE5D,MAAM,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,KAAK,IAAI,EAAE;QAChC,MAAM,QAAQ,GAAG,MAAM,SAAS,CAAC,SAAS,CAAC,CAAC;QAC5C,IAAI,CAAC,QAAQ,EAAE,CAAC;YACd,MAAM,IAAI,KAAK,CAAC,mDAAmD,SAAS,EAAE,CAAC,CAAC;QAClF,CAAC;QAED,iBAAiB;QACjB,MAAM,QAAQ,GAAG,QAAQ,CAAC,OAAO,CAAC,MAAM,CACtC,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,IAAI,KAAK,WAAW,CACxC,CAAC;QACF,MAAM,MAAM,GAAG,CAAC,GAAG,QAAQ,EAAE,GAAG,UAAU,CAAC,CAAC;QAE5C,QAAQ,CAAC,OAAO,GAAG,MAAM,CAAC;QAC1B,QAAQ,CAAC,YAAY,GAAG,MAAM,CAAC,MAAM,CAAC;QACtC,QAAQ,CAAC,UAAU,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;QAEjC,oCAAoC;QACpC,IAAI,SAAS,EAAE,CAAC;YACd,QAAQ,CAAC,KAAK,GAAG,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,WAAW,CAAC,CAAC;YACtE,QAAQ,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;YAC/B,QAAQ,CAAC,UAAU,GAAG,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC;QAC9C,CAAC;QAED,MAAM,SAAS,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAC;IACvC,CAAC,CAAC,CAAC;IAEH,gEAAgE;IAChE,UAAU,CAAC,GAAG,CAAC,SAAS,EAAE,IAAI,CAAC,KAAK,CAAC,GAAG,EAAE,GAAE,CAAC,CAAC,CAAC,CAAC;IAChD,OAAO,IAAI,CAAC;AACd,CAAC;AAED;;;GAGG;AACH,MAAM,CAAC,KAAK,UAAU,mBAAmB,CACvC,SAAiB,EACjB,WAAmB;IAEnB,MAAM,IAAI,GAAG,UAAU,CAAC,GAAG,CAAC,SAAS,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,CAAC;IAE5D,MAAM,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,KAAK,IAAI,EAAE;QAChC,MAAM,QAAQ,GAAG,MAAM,SAAS,CAAC,SAAS,CAAC,CAAC;QAC5C,IAAI,CAAC,QAAQ;YAAE,OAAO;QAEtB,MAAM,UAAU,GAAG,QAAQ,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,WAAW,CAAC,CAAC;QACxE,MAAM,OAAO,GAAG,QAAQ,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,WAAW,CAAC,CAAC;QACnE,IAAI,CAAC,UAAU,IAAI,CAAC,OAAO;YAAE,OAAO;QAEpC,QAAQ,CAAC,OAAO,GAAG,QAAQ,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,WAAW,CAAC,CAAC;QAC1E,QAAQ,CAAC,YAAY,GAAG,QAAQ,CAAC,OAAO,CAAC,MAAM,CAAC;QAChD,QAAQ,CAAC,KAAK,GAAG,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,WAAW,CAAC,CAAC;QACtE,QAAQ,CAAC,UAAU,GAAG,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC;QAC5C,QAAQ,CAAC,UAAU,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;QAEjC,MAAM,SAAS,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAC;IACvC,CAAC,CAAC,CAAC;IAEH,UAAU,CAAC,GAAG,CAAC,SAAS,EAAE,IAAI,CAAC,KAAK,CAAC,GAAG,EAAE,GAAE,CAAC,CAAC,CAAC,CAAC;IAChD,OAAO,IAAI,CAAC;AACd,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,YAAY,CAAC,OAAe,EAAE,QAAgB;IAC5D,MAAM,IAAI,GAAG,UAAU,CAAC,QAAQ,CAAC;SAC9B,MAAM,CAAC,QAAQ,CAAC;SAChB,MAAM,CAAC,KAAK,CAAC;SACb,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;IAEhB,OAAO,IAAI,CAAC,OAAO,EAAE,GAAG,IAAI,aAAa,CAAC,CAAC;AAC7C,CAAC;AAED,SAAS,YAAY,CAAC,KAAc;IAClC,IAAI,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,IAAI;QAAE,OAAO,KAAK,CAAC;IAE9D,MAAM,GAAG,GAAG,KAAgC,CAAC;IAC7C,IAAI,OAAO,GAAG,CAAC,MAAM,CAAC,KAAK,QAAQ;QAAE,OAAO,KAAK,CAAC;IAClD,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC;QAAE,OAAO,KAAK,CAAC;IAEjD,OAAO,IAAI,CAAC;AACd,CAAC"}

package/dist/storage/registry.d.ts

@@ -22,6 +22,10 @@ export declare function getRepo(registryPath: string, name: string): Promise<Rep
  * List all registered repos.
  */
 export declare function listRepos(registryPath: string): Promise<RepoMeta[]>;
+/**
+ * Partially update a repo's metadata (e.g., last_git_commit after freshness check).
+ */
+export declare function updateRepoMeta(registryPath: string, repoName: string, updates: Partial<Pick<RepoMeta, "last_git_commit" | "symbol_count" | "file_count" | "updated_at">>): Promise<void>;
 /**
  * Remove a repo from the registry.
  * Returns true if the repo existed and was removed, false otherwise.

package/dist/storage/registry.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"registry.d.ts","sourceRoot":"","sources":["../../src/storage/registry.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAC;AAEtD;;;GAGG;AACH,wBAAsB,YAAY,CAAC,YAAY,EAAE,MAAM,GAAG,OAAO,CAAC,QAAQ,CAAC,CAa1E;AAED;;;GAGG;AACH,wBAAsB,YAAY,CAChC,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,QAAQ,GACjB,OAAO,CAAC,IAAI,CAAC,CAcf;AAED;;GAEG;AACH,wBAAsB,YAAY,CAChC,YAAY,EAAE,MAAM,EACpB,IAAI,EAAE,QAAQ,GACb,OAAO,CAAC,IAAI,CAAC,CAKf;AAED;;;GAGG;AACH,wBAAsB,OAAO,CAC3B,YAAY,EAAE,MAAM,EACpB,IAAI,EAAE,MAAM,GACX,OAAO,CAAC,QAAQ,GAAG,IAAI,CAAC,CAG1B;AAED;;GAEG;AACH,wBAAsB,SAAS,CAC7B,YAAY,EAAE,MAAM,GACnB,OAAO,CAAC,QAAQ,EAAE,CAAC,CAGrB;AAED;;;GAGG;AACH,wBAAsB,UAAU,CAC9B,YAAY,EAAE,MAAM,EACpB,IAAI,EAAE,MAAM,GACX,OAAO,CAAC,OAAO,CAAC,CAWlB;AAED;;;GAGG;AACH,wBAAgB,WAAW,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAEpD"}
+{"version":3,"file":"registry.d.ts","sourceRoot":"","sources":["../../src/storage/registry.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAC;AAGtD;;;GAGG;AACH,wBAAsB,YAAY,CAAC,YAAY,EAAE,MAAM,GAAG,OAAO,CAAC,QAAQ,CAAC,CAa1E;AAED;;;GAGG;AACH,wBAAsB,YAAY,CAChC,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,QAAQ,GACjB,OAAO,CAAC,IAAI,CAAC,CAGf;AAED;;GAEG;AACH,wBAAsB,YAAY,CAChC,YAAY,EAAE,MAAM,EACpB,IAAI,EAAE,QAAQ,GACb,OAAO,CAAC,IAAI,CAAC,CAKf;AAED;;;GAGG;AACH,wBAAsB,OAAO,CAC3B,YAAY,EAAE,MAAM,EACpB,IAAI,EAAE,MAAM,GACX,OAAO,CAAC,QAAQ,GAAG,IAAI,CAAC,CAG1B;AAED;;GAEG;AACH,wBAAsB,SAAS,CAC7B,YAAY,EAAE,MAAM,GACnB,OAAO,CAAC,QAAQ,EAAE,CAAC,CAGrB;AAED;;GAEG;AACH,wBAAsB,cAAc,CAClC,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE,OAAO,CAAC,IAAI,CAAC,QAAQ,EAAE,iBAAiB,GAAG,cAAc,GAAG,YAAY,GAAG,YAAY,CAAC,CAAC,GACjG,OAAO,CAAC,IAAI,CAAC,CAOf;AAED;;;GAGG;AACH,wBAAsB,UAAU,CAC9B,YAAY,EAAE,MAAM,EACpB,IAAI,EAAE,MAAM,GACX,OAAO,CAAC,OAAO,CAAC,CAWlB;AAED;;;GAGG;AACH,wBAAgB,WAAW,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAEpD"}

package/dist/storage/registry.js

@@ -1,5 +1,6 @@
-import { readFile, writeFile, rename, mkdir, unlink } from "node:fs/promises";
-import { dirname, basename } from "node:path";
+import { readFile } from "node:fs/promises";
+import { basename } from "node:path";
+import { atomicWriteFile } from "./_shared.js";
 /**
  * Load the multi-repo registry from disk.
  * Returns an empty registry if the file doesn't exist or is invalid.
@@ -22,21 +23,8 @@ export async function loadRegistry(registryPath) {
  * Writes to a temp file first, then renames to prevent partial reads.
  */
 export async function saveRegistry(registryPath, registry) {
-    const dir = dirname(registryPath);
-    await mkdir(dir, { recursive: true });
-    const tmpPath = `${registryPath}.tmp.${Date.now()}.json`;
     const data = JSON.stringify(registry);
-    try {
-        await writeFile(tmpPath, data, "utf-8");
-        await rename(tmpPath, registryPath);
-    }
-    catch (err) {
-        try {
-            await unlink(tmpPath);
-        }
-        catch { /* cleanup best-effort */ }
-        throw err;
-    }
+    await atomicWriteFile(registryPath, data);
 }
 /**
  * Register or update a repo in the registry.
@@ -62,6 +50,18 @@ export async function listRepos(registryPath) {
     const registry = await loadRegistry(registryPath);
     return Object.values(registry.repos);
 }
+/**
+ * Partially update a repo's metadata (e.g., last_git_commit after freshness check).
+ */
+export async function updateRepoMeta(registryPath, repoName, updates) {
+    const registry = await loadRegistry(registryPath);
+    const existing = registry.repos[repoName];
+    if (!existing)
+        return;
+    Object.assign(existing, updates);
+    registry.updated_at = Date.now();
+    await saveRegistry(registryPath, registry);
+}
 /**
  * Remove a repo from the registry.
  * Returns true if the repo existed and was removed, false otherwise.

package/dist/storage/registry.js.map

@@ -1 +1 @@
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package/dist/storage/usage-stats.d.ts

@@ -14,6 +14,11 @@ export interface DailyStats {
     call_count: number;
     total_tokens: number;
 }
+export interface QueryTypeStats {
+    type: string;
+    query_count: number;
+    call_count: number;
+}
 export interface UsageStats {
     total_calls: number;
     total_sessions: number;
@@ -21,6 +26,7 @@ export interface UsageStats {
     tools: ToolStats[];
     top_repos: RepoStats[];
     daily: DailyStats[];
+    query_types: QueryTypeStats[];
     earliest_ts: number;
     latest_ts: number;
 }

package/dist/storage/usage-stats.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"usage-stats.d.ts","sourceRoot":"","sources":["../../src/storage/usage-stats.ts"],"names":[],"mappings":"AASA,MAAM,WAAW,SAAS;IACxB,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC;IACpB,mBAAmB,EAAE,MAAM,CAAC;IAC5B,cAAc,EAAE,MAAM,CAAC;IACvB,iBAAiB,EAAE,MAAM,CAAC;CAC3B;AAED,MAAM,WAAW,SAAS;IACxB,IAAI,EAAE,MAAM,CAAC;IACb,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,UAAU;IACzB,IAAI,EAAE,MAAM,CAAC;IACb,UAAU,EAAE,MAAM,CAAC;IACnB,YAAY,EAAE,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,cAAc;IAC7B,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC;IACpB,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,UAAU;IACzB,WAAW,EAAE,MAAM,CAAC;IACpB,cAAc,EAAE,MAAM,CAAC;IACvB,qBAAqB,EAAE,MAAM,CAAC;IAC9B,KAAK,EAAE,SAAS,EAAE,CAAC;IACnB,SAAS,EAAE,SAAS,EAAE,CAAC;IACvB,KAAK,EAAE,UAAU,EAAE,CAAC;IACpB,WAAW,EAAE,cAAc,EAAE,CAAC;IAC9B,WAAW,EAAE,MAAM,CAAC;IACpB,SAAS,EAAE,MAAM,CAAC;CACnB;AAyDD,wBAAsB,aAAa,CAAC,OAAO,CAAC,EAAE;IAC5C,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,IAAI,CAAC,EAAE,MAAM,CAAC;CACf,GAAG,OAAO,CAAC,UAAU,CAAC,CAuHtB;AAMD,wBAAgB,iBAAiB,CAAC,KAAK,EAAE,UAAU,GAAG,MAAM,CA0E3D"}

package/dist/storage/usage-stats.js

@@ -1,13 +1,9 @@
 import { readFile } from "node:fs/promises";
-import { join } from "node:path";
-import { homedir } from "node:os";
+import { getCumulativeSavings, getUsagePath } from "./usage-tracker.js";
+import { formatTable } from "../formatters.js";
 // ---------------------------------------------------------------------------
 // Loading
 // ---------------------------------------------------------------------------
-function getUsagePath() {
-    const dataDir = process.env["CODESIFT_DATA_DIR"] ?? join(homedir(), ".codesift");
-    return join(dataDir, "usage.jsonl");
-}
 function isValidEntry(value) {
     if (typeof value !== "object" || value === null)
         return false;
@@ -62,6 +58,7 @@ export async function getUsageStats(options) {
             tools: [],
             top_repos: [],
             daily: [],
+            query_types: [],
             earliest_ts: 0,
             latest_ts: 0,
         };
@@ -71,6 +68,9 @@ export async function getUsageStats(options) {
     const repoMap = new Map();
     const sessionSet = new Set();
     const dailyMap = new Map();
+    // codebase_retrieval query type breakdown
+    const queryTypeQueries = new Map(); // type → total query count
+    const queryTypeCalls = new Map(); // type → calls containing this type
     let earliest = Infinity;
     let latest = 0;
     for (const entry of entries) {
@@ -92,6 +92,22 @@ export async function getUsageStats(options) {
         dayStats.calls += 1;
         dayStats.tokens += entry.result_tokens;
         dailyMap.set(date, dayStats);
+        // codebase_retrieval query type breakdown
+        if (entry.tool === "codebase_retrieval") {
+            const types = entry.args_summary?.["query_types"];
+            if (Array.isArray(types)) {
+                const seenInCall = new Set();
+                for (const t of types) {
+                    if (typeof t === "string") {
+                        queryTypeQueries.set(t, (queryTypeQueries.get(t) ?? 0) + 1);
+                        seenInCall.add(t);
+                    }
+                }
+                for (const t of seenInCall) {
+                    queryTypeCalls.set(t, (queryTypeCalls.get(t) ?? 0) + 1);
+                }
+            }
+        }
         // Time range
         if (entry.ts < earliest)
             earliest = entry.ts;
@@ -120,6 +136,13 @@ export async function getUsageStats(options) {
     }))
         .sort((a, b) => a.date.localeCompare(b.date));
     const totalSessions = sessionSet.size;
+    const query_types = [...queryTypeQueries.entries()]
+        .map(([type, query_count]) => ({
+        type,
+        query_count,
+        call_count: queryTypeCalls.get(type) ?? 0,
+    }))
+        .sort((a, b) => b.query_count - a.query_count);
     return {
         total_calls: entries.length,
         total_sessions: totalSessions,
@@ -127,6 +150,7 @@ export async function getUsageStats(options) {
         tools,
         top_repos,
         daily,
+        query_types,
         earliest_ts: earliest,
         latest_ts: latest,
     };
@@ -150,12 +174,32 @@ export function formatUsageReport(stats) {
     lines.push("");
     // Tool breakdown
     lines.push("--- Tool Breakdown ---");
-    const maxToolLen = Math.max(...stats.tools.map((t) => t.tool.length), 4);
-    lines.push(`${"Tool".padEnd(maxToolLen)}  ${"Calls".padStart(6)}  ${"Tokens".padStart(8)}  ${"Avg ms".padStart(7)}  ${"Avg tok".padStart(7)}`);
-    for (const t of stats.tools) {
-        lines.push(`${t.tool.padEnd(maxToolLen)}  ${String(t.total_calls).padStart(6)}  ${String(t.total_result_tokens).padStart(8)}  ${String(t.avg_elapsed_ms).padStart(7)}  ${String(t.avg_result_tokens).padStart(7)}`);
-    }
+    const toolRows = stats.tools.map((t) => [
+        t.tool,
+        String(t.total_calls),
+        String(t.total_result_tokens),
+        String(t.avg_elapsed_ms),
+        String(t.avg_result_tokens),
+    ]);
+    lines.push(formatTable(["Tool", "Calls", "Tokens", "Avg ms", "Avg tok"], toolRows));
     lines.push("");
+    // codebase_retrieval query type breakdown
+    if (stats.query_types.length > 0) {
+        const crTool = stats.tools.find((t) => t.tool === "codebase_retrieval");
+        const totalQueries = stats.query_types.reduce((sum, qt) => sum + qt.query_count, 0);
+        lines.push("--- codebase_retrieval Query Types ---");
+        const qtRows = stats.query_types.map((qt) => {
+            const pct = totalQueries > 0 ? Math.round((qt.query_count / totalQueries) * 100) : 0;
+            return [
+                qt.type,
+                String(qt.query_count),
+                `${pct}%`,
+                `${qt.call_count}/${crTool?.total_calls ?? "?"}`,
+            ];
+        });
+        lines.push(formatTable(["Type", "Queries", "%", "In calls"], qtRows));
+        lines.push("");
+    }
     // Top repos
     if (stats.top_repos.length > 0) {
         lines.push("--- Top Repos ---");
@@ -175,6 +219,10 @@ export function formatUsageReport(stats) {
             lines.push(`  ... and ${stats.daily.length - 14} earlier days`);
         }
     }
+    const saved = getCumulativeSavings();
+    if (saved > 0) {
+        lines.push(`\nEstimated tokens saved this session: ${saved.toLocaleString()} (~$${(saved * 30 / 1_000_000).toFixed(2)} at Opus rates)`);
+    }
     return lines.join("\n");
 }
 //# sourceMappingURL=usage-stats.js.map