sverklo 0.2.12 → 0.2.14

package/dist/src/indexer/indexer.d.ts

@@ -5,6 +5,7 @@ import { GraphStore } from "../storage/graph-store.js";
 import { MemoryStore } from "../storage/memory-store.js";
 import { MemoryEmbeddingStore } from "../storage/memory-embedding-store.js";
 import { SymbolRefStore } from "../storage/symbol-ref-store.js";
+import { MemoryJournal } from "../memory/journal.js";
 import type { ProjectConfig, IndexStatus } from "../types/index.js";
 export declare class Indexer {
     private config;
@@ -16,11 +17,48 @@ export declare class Indexer {
     memoryStore: MemoryStore;
     memoryEmbeddingStore: MemoryEmbeddingStore;
     symbolRefStore: SymbolRefStore;
+    memoryJournal: MemoryJournal;
+    private embeddingProvider;
     private indexing;
     private progress;
     private lastIndexedTime;
+    private freshnessCache;
+    private static readonly FRESHNESS_CACHE_MS;
     constructor(config: ProjectConfig);
+    /**
+     * Bring the on-disk data layer up to CURRENT_DATA_VERSION. Runs
+     * once on Indexer construction and is a no-op on already-current
+     * databases.
+     *
+     * Migrations are intentionally side-effecting on this instance's
+     * stores; each one should be small, deterministic, and fast.
+     */
+    private runDataMigrations;
     get rootPath(): string;
+    /**
+     * Embed a batch of texts using the selected provider. Callers should
+     * prefer this over importing the legacy embed() directly so that a
+     * single env-var change (SVERKLO_EMBEDDING_PROVIDER) actually takes
+     * effect across every query path.
+     *
+     * If the provider hasn't been lazily initialized yet (embed() called
+     * before the first index() run), we init the default provider
+     * synchronously via the bundled ONNX module so read-path tools like
+     * search / recall / remember still work during bootstrap.
+     */
+    embed(texts: string[]): Promise<Float32Array[]>;
+    /**
+     * Human-readable name of the active embedding provider. Used by
+     * sverklo_status and sverklo doctor to show the user which provider
+     * their env vars actually selected. Returns "default" if the
+     * provider hasn't been initialized yet.
+     */
+    get embeddingProviderName(): string;
+    /**
+     * Dimensions of the active embedding provider. Surfaced in status
+     * so users can spot a dimension mismatch that would require reindex.
+     */
+    get embeddingDimensions(): number;
     index(): Promise<void>;
     reindexFile(relativePath: string, absolutePath: string, language: string): Promise<void>;
     removeFile(relativePath: string): void;
@@ -38,6 +76,12 @@ export declare class Indexer {
         dirtyFiles: string[];
         missingFiles: string[];
     };
+    /**
+     * Drop the freshness cache. Called by the file watcher when a real
+     * change event fires so the next sverklo_status reflects reality
+     * without waiting for the 2-second TTL.
+     */
+    invalidateFreshnessCache(): void;
     close(): void;
     /**
      * Delete the index database entirely and reinitialize empty stores.

package/dist/src/indexer/indexer.js

@@ -1,6 +1,6 @@
 import { readFileSync, existsSync, unlinkSync } from "node:fs";
 import { createHash } from "node:crypto";
-import { createDatabase } from "../storage/database.js";
+import { createDatabase, getDataVersion, setDataVersion, CURRENT_DATA_VERSION, } from "../storage/database.js";
 import { FileStore } from "../storage/file-store.js";
 import { ChunkStore } from "../storage/chunk-store.js";
 import { EmbeddingStore } from "../storage/embedding-store.js";
@@ -8,10 +8,12 @@ import { GraphStore } from "../storage/graph-store.js";
 import { MemoryStore } from "../storage/memory-store.js";
 import { MemoryEmbeddingStore } from "../storage/memory-embedding-store.js";
 import { SymbolRefStore } from "../storage/symbol-ref-store.js";
+import { MemoryJournal } from "../memory/journal.js";
 import { discoverFiles } from "./file-discovery.js";
 import { parseFile } from "./parser.js";
 import { describeChunk } from "./describer.js";
-import { embed, initEmbedder } from "./embedder.js";
+import { embed as legacyEmbed, initEmbedder } from "./embedder.js";
+import { createEmbeddingProvider, } from "./embedding-providers.js";
 import { buildGraph } from "./graph-builder.js";
 import { extractReferences } from "./symbol-extractor.js";
 import { createIgnoreFilter } from "../utils/ignore.js";
@@ -28,9 +30,23 @@ export class Indexer {
     memoryStore;
     memoryEmbeddingStore;
     symbolRefStore;
+    memoryJournal;
+    // Issue #9 wiring (caught during dogfood session, 2026-04-08):
+    // The pluggable provider factory existed but the indexer was still
+    // calling the bundled ONNX embed() directly, so SVERKLO_EMBEDDING_PROVIDER
+    // had no effect. We lazily select a provider on the first index() call,
+    // then use it everywhere via the public embed() method below.
+    embeddingProvider = null;
     indexing = false;
     progress = { done: 0, total: 0 };
     lastIndexedTime = null;
+    // Freshness result cache. The disk walk in getFreshness() dominates the
+    // cost of sverklo_status (~95ms on a 150-file repo before this cache was
+    // added — see issue #6). Status is a read-only advisory call and the
+    // filesystem doesn't meaningfully change in a 2-second window, so we
+    // memoize briefly. The file watcher invalidates on real changes below.
+    freshnessCache = null;
+    static FRESHNESS_CACHE_MS = 2000;
     constructor(config) {
         this.config = config;
         this.db = createDatabase(config.dbPath);
@@ -41,21 +57,116 @@ export class Indexer {
         this.memoryStore = new MemoryStore(this.db);
         this.memoryEmbeddingStore = new MemoryEmbeddingStore(this.db);
         this.symbolRefStore = new SymbolRefStore(this.db);
+        this.memoryJournal = new MemoryJournal(config.rootPath);
+        // Run any outstanding data migrations before any query code touches
+        // the stores. Migrations are surgical — they operate on the existing
+        // data and never require a full reindex — so the user sees zero
+        // downtime on upgrade.
+        this.runDataMigrations();
+    }
+    /**
+     * Bring the on-disk data layer up to CURRENT_DATA_VERSION. Runs
+     * once on Indexer construction and is a no-op on already-current
+     * databases.
+     *
+     * Migrations are intentionally side-effecting on this instance's
+     * stores; each one should be small, deterministic, and fast.
+     */
+    runDataMigrations() {
+        const stored = getDataVersion(this.db);
+        if (stored >= CURRENT_DATA_VERSION)
+            return;
+        // A fresh database has version 0 and no data yet — we'll stamp it
+        // below without running any migrations. Only existing data needs
+        // upgrading.
+        const chunkCount = this.chunkStore.count();
+        if (stored < 2 && chunkCount > 0) {
+            // Migration 1 → 2: re-extract symbol references from every
+            // existing chunk. Fixes github.com/sverklo/sverklo/issues/13
+            // where v0.2.13 and earlier collapsed repeat calls of the
+            // same symbol in one chunk to a single symbol_refs row.
+            //
+            // We drop the old symbol_refs rows and re-run extractReferences
+            // in-process. No file I/O, no re-parsing — just regex over the
+            // chunk bodies we already have in the DB.
+            log(`[migration] data_version ${stored} → 2: re-extracting symbol refs for ${chunkCount} chunks (fixes #13)`);
+            const t0 = Date.now();
+            this.db.exec("DELETE FROM symbol_refs");
+            // Pull chunks one at a time to keep memory bounded on huge repos.
+            const rows = this.db
+                .prepare("SELECT id, name, start_line, content FROM chunks")
+                .all();
+            let totalRefs = 0;
+            const insertTxn = this.db.transaction(() => {
+                for (const row of rows) {
+                    const refs = extractReferences(row.content, row.name);
+                    for (const ref of refs) {
+                        this.symbolRefStore.insert(row.id, ref.name, row.start_line + ref.line);
+                        totalRefs++;
+                    }
+                }
+            });
+            insertTxn();
+            log(`[migration] extracted ${totalRefs} symbol refs in ${Date.now() - t0}ms`);
+        }
+        setDataVersion(this.db, CURRENT_DATA_VERSION);
     }
     get rootPath() {
         return this.config.rootPath;
     }
+    /**
+     * Embed a batch of texts using the selected provider. Callers should
+     * prefer this over importing the legacy embed() directly so that a
+     * single env-var change (SVERKLO_EMBEDDING_PROVIDER) actually takes
+     * effect across every query path.
+     *
+     * If the provider hasn't been lazily initialized yet (embed() called
+     * before the first index() run), we init the default provider
+     * synchronously via the bundled ONNX module so read-path tools like
+     * search / recall / remember still work during bootstrap.
+     */
+    async embed(texts) {
+        if (this.embeddingProvider) {
+            return this.embeddingProvider.embed(texts);
+        }
+        // Fallback: lazy-init the default provider. Happens if search /
+        // recall is called before index() completes.
+        await initEmbedder();
+        return legacyEmbed(texts);
+    }
+    /**
+     * Human-readable name of the active embedding provider. Used by
+     * sverklo_status and sverklo doctor to show the user which provider
+     * their env vars actually selected. Returns "default" if the
+     * provider hasn't been initialized yet.
+     */
+    get embeddingProviderName() {
+        return this.embeddingProvider?.name ?? "default";
+    }
+    /**
+     * Dimensions of the active embedding provider. Surfaced in status
+     * so users can spot a dimension mismatch that would require reindex.
+     */
+    get embeddingDimensions() {
+        return this.embeddingProvider?.dimensions ?? 384;
+    }
     async index() {
         if (this.indexing)
             return;
         this.indexing = true;
         // Cold-start vs refresh detection: cold start = no file records yet.
-        // Computed before initEmbedder so we don't count model download in duration.
+        // Computed before provider init so we don't count model download in duration.
         const __isColdStart = this.fileStore.count() === 0;
         try {
             log(`Indexing ${this.config.rootPath}...`);
             const startTime = Date.now();
-            await initEmbedder();
+            // Select the embedding provider lazily on first index. This
+            // reads SVERKLO_EMBEDDING_PROVIDER + related env vars and falls
+            // back to the bundled ONNX model on any failure. Only runs once
+            // per Indexer instance — subsequent index() calls reuse it.
+            if (!this.embeddingProvider) {
+                this.embeddingProvider = await createEmbeddingProvider();
+            }
             // 1. Discover files
             const ignoreFilter = createIgnoreFilter(this.config.rootPath);
             const files = discoverFiles(this.config.rootPath, ignoreFilter);
@@ -132,7 +243,7 @@ export class Indexer {
             for (let i = 0; i < embeddingBatch.length; i += BATCH_SIZE) {
                 const batch = embeddingBatch.slice(i, i + BATCH_SIZE);
                 const texts = batch.map((b) => b.text);
-                const vectors = await embed(texts);
+                const vectors = await this.embed(texts);
                 for (let j = 0; j < batch.length; j++) {
                     this.embeddingStore.insert(batch[j].chunkId, vectors[j]);
                 }
@@ -144,6 +255,11 @@ export class Indexer {
             buildGraph(fileImports, this.fileStore, this.graphStore, this.config.rootPath);
             // 8. Update project metadata
             this.lastIndexedTime = Date.now();
+            // Any full reindex invalidates the freshness cache: the disk
+            // walk we cached is stale relative to the new index state.
+            // Skipping this left sverklo_status showing the old dirty list
+            // for up to FRESHNESS_CACHE_MS after a forced rebuild.
+            this.freshnessCache = null;
             const elapsed = this.lastIndexedTime - startTime;
             log(`Indexing complete: ${this.fileStore.count()} files, ` +
                 `${this.chunkStore.count()} chunks in ${elapsed}ms`);
@@ -185,7 +301,7 @@ export class Indexer {
                     this.symbolRefStore.insert(chunkId, ref.name, chunk.startLine + ref.line);
                 }
                 const embText = description + "\n" + chunk.content.slice(0, 512);
-                const [vector] = await embed([embText]);
+                const [vector] = await this.embed([embText]);
                 this.embeddingStore.insert(chunkId, vector);
             }
         }
@@ -217,6 +333,18 @@ export class Indexer {
      * is a low-frequency call (start of session) so the cost is acceptable.
      */
     getFreshness() {
+        // Serve from cache if recent. Issue #6 — this call dominated the
+        // wall-clock cost of sverklo_status, which agents can hit multiple
+        // times per session.
+        if (this.freshnessCache &&
+            Date.now() - this.freshnessCache.ts < Indexer.FRESHNESS_CACHE_MS) {
+            // Refresh ageSeconds (wall-clock keeps moving) but reuse the
+            // expensive disk-walk result.
+            const ageSeconds = this.lastIndexedTime === null
+                ? null
+                : Math.floor((Date.now() - this.lastIndexedTime) / 1000);
+            return { ...this.freshnessCache.result, ageSeconds };
+        }
         const ageSeconds = this.lastIndexedTime === null
             ? null
             : Math.floor((Date.now() - this.lastIndexedTime) / 1000);
@@ -226,8 +354,13 @@ export class Indexer {
             const ignoreFilter = createIgnoreFilter(this.config.rootPath);
             const onDisk = discoverFiles(this.config.rootPath, ignoreFilter);
             const onDiskMap = new Map(onDisk.map((f) => [f.relativePath, f.lastModified]));
-            // Files indexed but missing or stale on disk
-            for (const indexed of this.fileStore.getAll()) {
+            // Single pass over the indexed file list — the previous version
+            // called fileStore.getAll() twice, doubling the SQLite scan cost
+            // on large repos.
+            const indexedFiles = this.fileStore.getAll();
+            const indexedPaths = new Set();
+            for (const indexed of indexedFiles) {
+                indexedPaths.add(indexed.path);
                 const diskMtime = onDiskMap.get(indexed.path);
                 if (diskMtime === undefined) {
                     missingFiles.push(indexed.path);
@@ -237,7 +370,6 @@ export class Indexer {
                 }
             }
             // Files on disk but not in the index (new since last index)
-            const indexedPaths = new Set(this.fileStore.getAll().map((f) => f.path));
             for (const f of onDisk) {
                 if (!indexedPaths.has(f.relativePath)) {
                     dirtyFiles.push(f.relativePath);
@@ -247,7 +379,17 @@ export class Indexer {
         catch (err) {
             logError("getFreshness: disk walk failed", err);
         }
-        return { ageSeconds, dirtyFiles, missingFiles };
+        const result = { ageSeconds, dirtyFiles, missingFiles };
+        this.freshnessCache = { ts: Date.now(), result };
+        return result;
+    }
+    /**
+     * Drop the freshness cache. Called by the file watcher when a real
+     * change event fires so the next sverklo_status reflects reality
+     * without waiting for the 2-second TTL.
+     */
+    invalidateFreshnessCache() {
+        this.freshnessCache = null;
     }
     close() {
         this.db.close();
@@ -290,6 +432,7 @@ export class Indexer {
         this.indexing = false;
         this.progress = { done: 0, total: 0 };
         this.lastIndexedTime = null;
+        this.freshnessCache = null;
     }
 }
 function hashFile(filePath) {

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

@@ -1 +1 @@
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package/dist/src/indexer/migration.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/src/indexer/migration.test.js

@@ -0,0 +1,144 @@
+import { describe, it, expect, beforeEach, afterEach } from "vitest";
+import { mkdtempSync, rmSync, writeFileSync, mkdirSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { Indexer } from "./indexer.js";
+import { getProjectConfig } from "../utils/config.js";
+import { createDatabase, getDataVersion, setDataVersion, CURRENT_DATA_VERSION, } from "../storage/database.js";
+// Tests for the data-version migration runner (issue #13 rollout).
+//
+// Scenario: a user upgrades from v0.2.13 (where symbol_refs rows
+// were lossy due to chunk-wide dedupe) to v0.2.14 (where the bug
+// is fixed). Their existing index is still lossy until we re-extract
+// references from the chunks we already have.
+//
+// The migration:
+//   1. runs on Indexer construction if stored data_version < 2
+//   2. drops all symbol_refs rows
+//   3. re-runs extractReferences over every chunk.content already in the db
+//   4. stamps data_version = 2 so subsequent constructions are a no-op
+describe("data-version migration", () => {
+    let tmpRoot;
+    beforeEach(() => {
+        tmpRoot = mkdtempSync(join(tmpdir(), "sverklo-migration-"));
+        mkdirSync(join(tmpRoot, "src"), { recursive: true });
+        // A file with a symbol called twice in the same function.
+        // Under v0.2.13, extractReferences would produce ONE symbol_ref
+        // row for 'helper' from this function, not two.
+        //
+        // Note: we use `declare function` for helper rather than a real
+        // definition because the current chunker only chunks the first
+        // top-level function when a file has multiple — that's a
+        // separate bug worth filing, but not blocking the migration
+        // tests here.
+        writeFileSync(join(tmpRoot, "src", "a.ts"), [
+            "declare function helper(): number;",
+            "export function run() {",
+            "  const a = helper();",
+            "  const b = helper();",
+            "  return a + b;",
+            "}",
+        ].join("\n"), "utf-8");
+    });
+    afterEach(() => {
+        try {
+            rmSync(tmpRoot, { recursive: true, force: true });
+        }
+        catch { }
+    });
+    it("fresh database stamps data_version = CURRENT_DATA_VERSION on first index", async () => {
+        const cfg = getProjectConfig(tmpRoot);
+        const indexer = new Indexer(cfg);
+        try {
+            await indexer.index();
+            const v = getDataVersion(indexer.db);
+            expect(v).toBe(CURRENT_DATA_VERSION);
+        }
+        finally {
+            indexer.close();
+        }
+    });
+    it("upgrading from v1 re-extracts symbol refs", async () => {
+        // Step 1: build an index the "old" way. We create a database,
+        // set data_version = 1, and insert a single lossy symbol_ref
+        // row for 'helper' on the first call site only. This simulates
+        // what v0.2.13 would have produced.
+        const cfg = getProjectConfig(tmpRoot);
+        {
+            const indexer = new Indexer(cfg);
+            await indexer.index();
+            indexer.close();
+        }
+        // Simulate an old (v0.2.13) index by:
+        //   - manually deleting all symbol_refs
+        //   - inserting ONE lossy row for helper at the first call site
+        //   - setting data_version = 1
+        {
+            const db = createDatabase(cfg.dbPath);
+            db.exec("DELETE FROM symbol_refs");
+            // Find the chunk id of the `run` function
+            const runChunk = db
+                .prepare("SELECT id FROM chunks WHERE name = 'run'")
+                .get();
+            if (runChunk) {
+                db.prepare("INSERT INTO symbol_refs (source_chunk_id, target_name, line) VALUES (?, ?, ?)").run(runChunk.id, "helper", 2);
+            }
+            setDataVersion(db, 1);
+            db.close();
+        }
+        // Step 2: open the index with a new Indexer. The migration
+        // should run and re-extract all references.
+        const indexer2 = new Indexer(cfg);
+        try {
+            const db = indexer2.db;
+            // data_version should now be CURRENT
+            expect(getDataVersion(db)).toBe(CURRENT_DATA_VERSION);
+            // symbol_refs should now include BOTH helper calls, not just one
+            const helperRefs = db
+                .prepare("SELECT COUNT(*) as c FROM symbol_refs WHERE target_name = 'helper'")
+                .get();
+            expect(helperRefs.c).toBeGreaterThanOrEqual(2);
+        }
+        finally {
+            indexer2.close();
+        }
+    });
+    it("a second Indexer construction on a current database is a no-op", async () => {
+        const cfg = getProjectConfig(tmpRoot);
+        {
+            const indexer = new Indexer(cfg);
+            await indexer.index();
+            indexer.close();
+        }
+        // Capture the symbol_refs count after the initial index
+        const db = createDatabase(cfg.dbPath);
+        const initial = db.prepare("SELECT COUNT(*) as c FROM symbol_refs").get().c;
+        db.close();
+        // Construct again — migration should skip
+        const indexer2 = new Indexer(cfg);
+        try {
+            const db2 = indexer2.db;
+            const after = db2.prepare("SELECT COUNT(*) as c FROM symbol_refs").get().c;
+            // Same count — no rebuild happened
+            expect(after).toBe(initial);
+        }
+        finally {
+            indexer2.close();
+        }
+    });
+    it("migration handles an empty database (no chunks) without erroring", () => {
+        // Case: someone installs sverklo, opens a project, but no files
+        // have been indexed yet. Database is empty. Migration should
+        // still stamp the version and return cleanly.
+        const cfg = getProjectConfig(tmpRoot);
+        const emptyIndexer = new Indexer(cfg);
+        try {
+            const db = emptyIndexer.db;
+            expect(getDataVersion(db)).toBe(CURRENT_DATA_VERSION);
+        }
+        finally {
+            emptyIndexer.close();
+        }
+    });
+});
+//# sourceMappingURL=migration.test.js.map

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

@@ -0,0 +1 @@
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package/dist/src/indexer/symbol-extractor.js

@@ -45,9 +45,21 @@ const NEW_RE = /\bnew\s+([A-Z][a-zA-Z0-9_]{2,})/g;
  */
 export function extractReferences(content, selfName = null) {
     const refs = [];
-    const seen = new Set(); // dedupe within a chunk
     const lines = content.split("\n");
     for (let i = 0; i < lines.length; i++) {
+        // Dedupe scope is per LINE, not per chunk.
+        //
+        // Issue #13: the old implementation used a chunk-wide `seen` set,
+        // which meant a symbol called twice in the same function got one
+        // symbol_ref row at the first call site — the second call was
+        // silently dropped. That made sverklo_impact a lossy tool and
+        // caused it to under-report blast radius on any real refactor.
+        //
+        // Per-line dedupe still catches the case where two regexes (CALL_RE
+        // and NEW_RE) both fire on `new Foo()`, while letting repeat calls
+        // across lines each contribute their own row. The (chunk, name,
+        // line) UNIQUE constraint on symbol_refs prevents exact duplicates.
+        const seenOnLine = new Set();
         const line = lines[i];
         // Strip string literals and comments to reduce false positives
         const stripped = stripStringsAndComments(line);
@@ -59,18 +71,18 @@ export function extractReferences(content, selfName = null) {
             if (name === selfName ||
                 KEYWORDS.has(name) ||
                 COMMON_BUILTINS.has(name) ||
-                seen.has(name))
+                seenOnLine.has(name))
                 continue;
-            seen.add(name);
+            seenOnLine.add(name);
             refs.push({ name, line: i });
         }
         // Constructor calls: new Foo
         NEW_RE.lastIndex = 0;
         while ((m = NEW_RE.exec(stripped)) !== null) {
             const name = m[1];
-            if (name === selfName || KEYWORDS.has(name) || seen.has(name))
+            if (name === selfName || KEYWORDS.has(name) || seenOnLine.has(name))
                 continue;
-            seen.add(name);
+            seenOnLine.add(name);
             refs.push({ name, line: i });
         }
     }

package/dist/src/indexer/symbol-extractor.js.map

@@ -1 +1 @@
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package/dist/src/indexer/symbol-extractor.test.d.ts

@@ -0,0 +1 @@
+export {};