@neuralsea/workspace-indexer 0.3.2 → 0.3.4

package/dist/{chunk-GGL3XTMV.js → chunk-ENM3P2PS.js}

@@ -1621,6 +1621,16 @@ var RepoFileIndexer = class {
       return;
     }
     this.emit({ type: "repo/index/file/start", repoRoot: this.repoRoot, path: posixRelPath });
+    const stage = (stageName, stageStartedAt) => {
+      this.emit({
+        type: "repo/index/file/stage",
+        repoRoot: this.repoRoot,
+        path: posixRelPath,
+        stage: stageName,
+        ms: Date.now() - stageStartedAt
+      });
+    };
+    const readStartedAt = Date.now();
     const abs = path9.join(this.repoRoot, fromPosixPath(posixRelPath));
     let stat;
     try {
@@ -1644,16 +1654,20 @@ var RepoFileIndexer = class {
     }
     const raw = buf.toString("utf8");
     const redacted = this.applyRedactions(raw);
+    stage("read", readStartedAt);
     const fileHash = sha256Hex(redacted);
     const prev = this.store.getFileHash(posixRelPath);
     if (prev === fileHash) {
       this.emit({ type: "repo/index/file/skip", repoRoot: this.repoRoot, path: posixRelPath, reason: "unchanged" });
       return;
     }
+    const chunkStartedAt = Date.now();
     const { language, chunks } = chunkSource(posixRelPath, redacted, this.config.chunk);
+    stage("chunk", chunkStartedAt);
     let imports = [];
     let exports = [];
     if (language === "typescript" || language === "javascript") {
+      const relationsStartedAt = Date.now();
       const rel = extractTsRelations(posixRelPath, redacted);
       imports = rel.imports;
       exports = rel.exports;
@@ -1661,12 +1675,14 @@ var RepoFileIndexer = class {
       this.store.setEdges(posixRelPath, "export", rel.exports);
       this.workspaceStore?.setEdges(this.repoId, posixRelPath, "import", rel.imports);
       this.workspaceStore?.setEdges(this.repoId, posixRelPath, "export", rel.exports);
+      stage("relations", relationsStartedAt);
     } else {
       this.store.setEdges(posixRelPath, "import", []);
       this.store.setEdges(posixRelPath, "export", []);
       this.workspaceStore?.setEdges(this.repoId, posixRelPath, "import", []);
       this.workspaceStore?.setEdges(this.repoId, posixRelPath, "export", []);
     }
+    const synopsisStartedAt = Date.now();
     const synopsisText = buildSynopsis(posixRelPath, language, redacted);
     const synopsis = synopsisText.trim() ? [
       {
@@ -1691,14 +1707,18 @@ var RepoFileIndexer = class {
       }
     ] : [];
     const combined = [...synopsis, ...headerChunk, ...chunks.map((c) => ({ ...c, kind: "chunk" }))];
+    stage("synopsis", synopsisStartedAt);
+    const embedStartedAt = Date.now();
     const embedTexts = [];
     const embedPlan = [];
     const embeddings = combined.map(() => null);
+    let cached2 = 0;
     for (let i = 0; i < combined.length; i++) {
       const ch = combined[i];
-      const cached2 = this.embeddingCache.get(this.embedder.id, ch.contentHash);
-      if (cached2) {
-        embeddings[i] = cached2;
+      const cachedEmb = this.embeddingCache.get(this.embedder.id, ch.contentHash);
+      if (cachedEmb) {
+        embeddings[i] = cachedEmb;
+        cached2++;
         continue;
       }
       embedTexts.push(
@@ -1730,11 +1750,22 @@ ${ch.text}`
         this.embeddingCache.put(this.embedder.id, plan.contentHash, vecs[j]);
       }
     }
+    this.emit({
+      type: "repo/index/file/embed/done",
+      repoRoot: this.repoRoot,
+      path: posixRelPath,
+      chunks: combined.length,
+      cached: cached2,
+      computed: embedTexts.length,
+      ms: Date.now() - embedStartedAt
+    });
+    stage("embed", embedStartedAt);
     const fileMtime = stat.mtimeMs;
     const ftsMode = this.config.storage.ftsMode;
     const storeText = this.config.storage.storeText;
     const oldChunkIds = this.store.listChunksForFile(posixRelPath).map((r) => r.id);
     const points = [];
+    const storeStartedAt = Date.now();
     const rows = combined.map((ch, i) => {
       const id = sha256Hex(
         `${this.repoId}:${posixRelPath}:${ch.kind}:${ch.startLine}:${ch.endLine}:${ch.contentHash}`
@@ -1762,7 +1793,19 @@ ${ch.text}`
     this.store.replaceChunksForFile(posixRelPath, rows);
     this.workspaceStore?.upsertFile(this.repoId, posixRelPath, fileHash, fileMtime, language, stat.size);
     this.workspaceStore?.replaceChunksForFile(this.repoId, this.repoRoot, posixRelPath, rows);
+    stage("store", storeStartedAt);
+    const symbolsStartedAt = Date.now();
     const symbolOut = await this.indexSymbolsIfEnabled(posixRelPath, language, redacted, fileHash);
+    this.emit({
+      type: "repo/index/file/symbols",
+      repoRoot: this.repoRoot,
+      path: posixRelPath,
+      symbols: symbolOut?.symbols?.length ?? 0,
+      edges: symbolOut?.edges?.length ?? 0,
+      ms: Date.now() - symbolsStartedAt
+    });
+    stage("symbols", symbolsStartedAt);
+    const graphStartedAt = Date.now();
     const head = this.getHead();
     if (this.graphStore && head) {
       await this.graphStore.replaceFileGraph({
@@ -1778,7 +1821,10 @@ ${ch.text}`
         symbolEdges: (symbolOut?.edges ?? []).map((e) => ({ fromId: e.fromId, toId: e.toId, kind: e.kind }))
       }).catch(() => void 0);
     }
+    stage("graph", graphStartedAt);
+    const vectorStartedAt = Date.now();
     await this.ensureVectorUpToDate(points, oldChunkIds);
+    stage("vector", vectorStartedAt);
     this.emit({
       type: "repo/index/file/done",
       repoRoot: this.repoRoot,
@@ -2389,11 +2435,14 @@ var RepoIndexer = class {
     const uniq3 = Array.from(new Set(posixPaths)).slice(0, maxFiles);
     for (const p of uniq3) {
       if (opts?.signal?.aborted) return;
+      const startedAt = Date.now();
+      this.emitProgress({ type: "repo/symbolGraph/expand/start", repoRoot: this.repoRoot, path: p });
       const abs = path12.join(this.repoRoot, p.split("/").join(path12.sep));
       let text = "";
       try {
         text = fs9.readFileSync(abs, "utf8");
       } catch {
+        this.emitProgress({ type: "repo/symbolGraph/expand/done", repoRoot: this.repoRoot, path: p, edges: 0, ms: Date.now() - startedAt });
         continue;
       }
       const contentHash = this.store.getFileHash(p) ?? void 0;
@@ -2411,6 +2460,7 @@ var RepoIndexer = class {
         fromPath: p,
         edges: normalized.map((e) => ({ fromId: e.fromId, toId: e.toId, kind: e.kind, toPath: e.toPath }))
       }).catch(() => void 0);
+      this.emitProgress({ type: "repo/symbolGraph/expand/done", repoRoot: this.repoRoot, path: p, edges: normalized.length, ms: Date.now() - startedAt });
     }
   }
   async watch() {
@@ -3362,8 +3412,8 @@ var Neo4jGraphStore = class {
         const stmts = [
           `CREATE CONSTRAINT ${Repo}_repo_id IF NOT EXISTS FOR (r:${Repo}) REQUIRE r.repo_id IS UNIQUE`,
           `CREATE CONSTRAINT ${Symbol}_id IF NOT EXISTS FOR (s:${Symbol}) REQUIRE s.id IS UNIQUE`,
-          `CREATE CONSTRAINT ${External}_key IF NOT EXISTS FOR (e:${External}) REQUIRE (e.repo_id, e.kind, e.value) IS NODE KEY`,
-          `CREATE CONSTRAINT ${File}_key IF NOT EXISTS FOR (f:${File}) REQUIRE (f.repo_id, f.path) IS NODE KEY`
+          `CREATE CONSTRAINT ${External}_key IF NOT EXISTS FOR (e:${External}) REQUIRE e.key IS UNIQUE`,
+          `CREATE CONSTRAINT ${File}_key IF NOT EXISTS FOR (f:${File}) REQUIRE f.key IS UNIQUE`
         ];
         for (const q of stmts) {
           try {
@@ -3489,10 +3539,18 @@ var Neo4jGraphStore = class {
       await s.run(
         `MERGE (r:${Repo} {repo_id:$repoId})
          SET r.repo_root=$repoRoot, r.commit=$commit, r.branch=$branch, r.updated_at=timestamp()
-         MERGE (f:${File} {repo_id:$repoId, path:$path})
-         SET f.repo_root=$repoRoot, f.language=$language, f.updated_at=timestamp()
+         MERGE (f:${File} {key:$fileKey})
+         SET f.repo_id=$repoId, f.path=$path, f.repo_root=$repoRoot, f.language=$language, f.updated_at=timestamp()
          MERGE (r)-[:HAS_FILE]->(f)`,
-        { repoId: update.repoId, repoRoot: update.repoRoot, commit: update.commit, branch: update.branch, path: update.path, language: update.language }
+        {
+          repoId: update.repoId,
+          repoRoot: update.repoRoot,
+          commit: update.commit,
+          branch: update.branch,
+          path: update.path,
+          language: update.language,
+          fileKey: `${update.repoId}:${update.path}`
+        }
       );
       const fileEdges = [
         ...update.imports.map((v) => ({ kind: "import", value: v })),
@@ -3502,9 +3560,14 @@ var Neo4jGraphStore = class {
       await s.run(
         `MATCH (f:${File} {repo_id:$repoId, path:$path})
          UNWIND $edges AS e
-         MERGE (x:${External} {repo_id:$repoId, kind:e.kind, value:e.value})
+         MERGE (x:${External} {key:e.key})
+         SET x.repo_id=$repoId, x.kind=e.kind, x.value=e.value
          MERGE (f)-[:FILE_EDGE {kind:e.kind}]->(x)`,
-        { repoId: update.repoId, path: update.path, edges: fileEdges }
+        {
+          repoId: update.repoId,
+          path: update.path,
+          edges: fileEdges.map((e) => ({ ...e, key: `${update.repoId}:${e.kind}:${e.value}` }))
+        }
       ).catch(() => void 0);
       await s.run(
         `MATCH (f:${File} {repo_id:$repoId, path:$path})-[r:FILE_EDGE]->(x:${External})
@@ -4223,11 +4286,14 @@ var WorkspaceIndexer = class {
           if (seeds.length >= 4) break;
         }
         if (seeds.length > 0) {
+          const gs = Date.now();
+          this.emitProgress({ type: "workspace/retrieve/graph/start", workspaceRoot: this.workspaceRoot, seeds: seeds.length });
           graphNeighborFiles = await this.graphStore.neighborFiles({
             seeds,
             limit: profile.name === "architecture" ? 16 : 10,
             kinds: ["definition", "reference", "implementation", "typeDefinition"]
           });
+          this.emitProgress({ type: "workspace/retrieve/graph/done", workspaceRoot: this.workspaceRoot, neighbors: graphNeighborFiles.length, ms: Date.now() - gs });
         }
       }
     } catch {

package/dist/cli.cjs

@@ -1604,6 +1604,16 @@ var RepoFileIndexer = class {
       return;
     }
     this.emit({ type: "repo/index/file/start", repoRoot: this.repoRoot, path: posixRelPath });
+    const stage = (stageName, stageStartedAt) => {
+      this.emit({
+        type: "repo/index/file/stage",
+        repoRoot: this.repoRoot,
+        path: posixRelPath,
+        stage: stageName,
+        ms: Date.now() - stageStartedAt
+      });
+    };
+    const readStartedAt = Date.now();
     const abs = import_node_path9.default.join(this.repoRoot, fromPosixPath(posixRelPath));
     let stat;
     try {
@@ -1627,16 +1637,20 @@ var RepoFileIndexer = class {
     }
     const raw = buf.toString("utf8");
     const redacted = this.applyRedactions(raw);
+    stage("read", readStartedAt);
     const fileHash = sha256Hex(redacted);
     const prev = this.store.getFileHash(posixRelPath);
     if (prev === fileHash) {
       this.emit({ type: "repo/index/file/skip", repoRoot: this.repoRoot, path: posixRelPath, reason: "unchanged" });
       return;
     }
+    const chunkStartedAt = Date.now();
     const { language, chunks } = chunkSource(posixRelPath, redacted, this.config.chunk);
+    stage("chunk", chunkStartedAt);
     let imports = [];
     let exports2 = [];
     if (language === "typescript" || language === "javascript") {
+      const relationsStartedAt = Date.now();
       const rel = extractTsRelations(posixRelPath, redacted);
       imports = rel.imports;
       exports2 = rel.exports;
@@ -1644,12 +1658,14 @@ var RepoFileIndexer = class {
       this.store.setEdges(posixRelPath, "export", rel.exports);
       this.workspaceStore?.setEdges(this.repoId, posixRelPath, "import", rel.imports);
       this.workspaceStore?.setEdges(this.repoId, posixRelPath, "export", rel.exports);
+      stage("relations", relationsStartedAt);
     } else {
       this.store.setEdges(posixRelPath, "import", []);
       this.store.setEdges(posixRelPath, "export", []);
       this.workspaceStore?.setEdges(this.repoId, posixRelPath, "import", []);
       this.workspaceStore?.setEdges(this.repoId, posixRelPath, "export", []);
     }
+    const synopsisStartedAt = Date.now();
     const synopsisText = buildSynopsis(posixRelPath, language, redacted);
     const synopsis = synopsisText.trim() ? [
       {
@@ -1674,14 +1690,18 @@ var RepoFileIndexer = class {
       }
     ] : [];
     const combined = [...synopsis, ...headerChunk, ...chunks.map((c) => ({ ...c, kind: "chunk" }))];
+    stage("synopsis", synopsisStartedAt);
+    const embedStartedAt = Date.now();
     const embedTexts = [];
     const embedPlan = [];
     const embeddings = combined.map(() => null);
+    let cached2 = 0;
     for (let i = 0; i < combined.length; i++) {
       const ch = combined[i];
-      const cached2 = this.embeddingCache.get(this.embedder.id, ch.contentHash);
-      if (cached2) {
-        embeddings[i] = cached2;
+      const cachedEmb = this.embeddingCache.get(this.embedder.id, ch.contentHash);
+      if (cachedEmb) {
+        embeddings[i] = cachedEmb;
+        cached2++;
         continue;
       }
       embedTexts.push(
@@ -1713,11 +1733,22 @@ ${ch.text}`
         this.embeddingCache.put(this.embedder.id, plan.contentHash, vecs[j]);
       }
     }
+    this.emit({
+      type: "repo/index/file/embed/done",
+      repoRoot: this.repoRoot,
+      path: posixRelPath,
+      chunks: combined.length,
+      cached: cached2,
+      computed: embedTexts.length,
+      ms: Date.now() - embedStartedAt
+    });
+    stage("embed", embedStartedAt);
     const fileMtime = stat.mtimeMs;
     const ftsMode = this.config.storage.ftsMode;
     const storeText = this.config.storage.storeText;
     const oldChunkIds = this.store.listChunksForFile(posixRelPath).map((r) => r.id);
     const points = [];
+    const storeStartedAt = Date.now();
     const rows = combined.map((ch, i) => {
       const id = sha256Hex(
         `${this.repoId}:${posixRelPath}:${ch.kind}:${ch.startLine}:${ch.endLine}:${ch.contentHash}`
@@ -1745,7 +1776,19 @@ ${ch.text}`
     this.store.replaceChunksForFile(posixRelPath, rows);
     this.workspaceStore?.upsertFile(this.repoId, posixRelPath, fileHash, fileMtime, language, stat.size);
     this.workspaceStore?.replaceChunksForFile(this.repoId, this.repoRoot, posixRelPath, rows);
+    stage("store", storeStartedAt);
+    const symbolsStartedAt = Date.now();
     const symbolOut = await this.indexSymbolsIfEnabled(posixRelPath, language, redacted, fileHash);
+    this.emit({
+      type: "repo/index/file/symbols",
+      repoRoot: this.repoRoot,
+      path: posixRelPath,
+      symbols: symbolOut?.symbols?.length ?? 0,
+      edges: symbolOut?.edges?.length ?? 0,
+      ms: Date.now() - symbolsStartedAt
+    });
+    stage("symbols", symbolsStartedAt);
+    const graphStartedAt = Date.now();
     const head = this.getHead();
     if (this.graphStore && head) {
       await this.graphStore.replaceFileGraph({
@@ -1761,7 +1804,10 @@ ${ch.text}`
         symbolEdges: (symbolOut?.edges ?? []).map((e) => ({ fromId: e.fromId, toId: e.toId, kind: e.kind }))
       }).catch(() => void 0);
     }
+    stage("graph", graphStartedAt);
+    const vectorStartedAt = Date.now();
     await this.ensureVectorUpToDate(points, oldChunkIds);
+    stage("vector", vectorStartedAt);
     this.emit({
       type: "repo/index/file/done",
       repoRoot: this.repoRoot,
@@ -2401,11 +2447,14 @@ var RepoIndexer = class {
     const uniq3 = Array.from(new Set(posixPaths)).slice(0, maxFiles);
     for (const p of uniq3) {
       if (opts?.signal?.aborted) return;
+      const startedAt = Date.now();
+      this.emitProgress({ type: "repo/symbolGraph/expand/start", repoRoot: this.repoRoot, path: p });
       const abs = import_node_path12.default.join(this.repoRoot, p.split("/").join(import_node_path12.default.sep));
       let text = "";
       try {
         text = import_node_fs9.default.readFileSync(abs, "utf8");
       } catch {
+        this.emitProgress({ type: "repo/symbolGraph/expand/done", repoRoot: this.repoRoot, path: p, edges: 0, ms: Date.now() - startedAt });
         continue;
       }
       const contentHash = this.store.getFileHash(p) ?? void 0;
@@ -2423,6 +2472,7 @@ var RepoIndexer = class {
         fromPath: p,
         edges: normalized.map((e) => ({ fromId: e.fromId, toId: e.toId, kind: e.kind, toPath: e.toPath }))
       }).catch(() => void 0);
+      this.emitProgress({ type: "repo/symbolGraph/expand/done", repoRoot: this.repoRoot, path: p, edges: normalized.length, ms: Date.now() - startedAt });
     }
   }
   async watch() {
@@ -3375,8 +3425,8 @@ var Neo4jGraphStore = class {
         const stmts = [
           `CREATE CONSTRAINT ${Repo}_repo_id IF NOT EXISTS FOR (r:${Repo}) REQUIRE r.repo_id IS UNIQUE`,
           `CREATE CONSTRAINT ${Symbol2}_id IF NOT EXISTS FOR (s:${Symbol2}) REQUIRE s.id IS UNIQUE`,
-          `CREATE CONSTRAINT ${External}_key IF NOT EXISTS FOR (e:${External}) REQUIRE (e.repo_id, e.kind, e.value) IS NODE KEY`,
-          `CREATE CONSTRAINT ${File}_key IF NOT EXISTS FOR (f:${File}) REQUIRE (f.repo_id, f.path) IS NODE KEY`
+          `CREATE CONSTRAINT ${External}_key IF NOT EXISTS FOR (e:${External}) REQUIRE e.key IS UNIQUE`,
+          `CREATE CONSTRAINT ${File}_key IF NOT EXISTS FOR (f:${File}) REQUIRE f.key IS UNIQUE`
         ];
         for (const q of stmts) {
           try {
@@ -3502,10 +3552,18 @@ var Neo4jGraphStore = class {
       await s.run(
         `MERGE (r:${Repo} {repo_id:$repoId})
          SET r.repo_root=$repoRoot, r.commit=$commit, r.branch=$branch, r.updated_at=timestamp()
-         MERGE (f:${File} {repo_id:$repoId, path:$path})
-         SET f.repo_root=$repoRoot, f.language=$language, f.updated_at=timestamp()
+         MERGE (f:${File} {key:$fileKey})
+         SET f.repo_id=$repoId, f.path=$path, f.repo_root=$repoRoot, f.language=$language, f.updated_at=timestamp()
          MERGE (r)-[:HAS_FILE]->(f)`,
-        { repoId: update.repoId, repoRoot: update.repoRoot, commit: update.commit, branch: update.branch, path: update.path, language: update.language }
+        {
+          repoId: update.repoId,
+          repoRoot: update.repoRoot,
+          commit: update.commit,
+          branch: update.branch,
+          path: update.path,
+          language: update.language,
+          fileKey: `${update.repoId}:${update.path}`
+        }
       );
       const fileEdges = [
         ...update.imports.map((v) => ({ kind: "import", value: v })),
@@ -3515,9 +3573,14 @@ var Neo4jGraphStore = class {
       await s.run(
         `MATCH (f:${File} {repo_id:$repoId, path:$path})
          UNWIND $edges AS e
-         MERGE (x:${External} {repo_id:$repoId, kind:e.kind, value:e.value})
+         MERGE (x:${External} {key:e.key})
+         SET x.repo_id=$repoId, x.kind=e.kind, x.value=e.value
          MERGE (f)-[:FILE_EDGE {kind:e.kind}]->(x)`,
-        { repoId: update.repoId, path: update.path, edges: fileEdges }
+        {
+          repoId: update.repoId,
+          path: update.path,
+          edges: fileEdges.map((e) => ({ ...e, key: `${update.repoId}:${e.kind}:${e.value}` }))
+        }
       ).catch(() => void 0);
       await s.run(
         `MATCH (f:${File} {repo_id:$repoId, path:$path})-[r:FILE_EDGE]->(x:${External})
@@ -4235,11 +4298,14 @@ var WorkspaceIndexer = class {
           if (seeds.length >= 4) break;
         }
         if (seeds.length > 0) {
+          const gs = Date.now();
+          this.emitProgress({ type: "workspace/retrieve/graph/start", workspaceRoot: this.workspaceRoot, seeds: seeds.length });
           graphNeighborFiles = await this.graphStore.neighborFiles({
             seeds,
             limit: profile.name === "architecture" ? 16 : 10,
             kinds: ["definition", "reference", "implementation", "typeDefinition"]
           });
+          this.emitProgress({ type: "workspace/retrieve/graph/done", workspaceRoot: this.workspaceRoot, neighbors: graphNeighborFiles.length, ms: Date.now() - gs });
         }
       }
     } catch {

package/dist/cli.js

@@ -5,7 +5,7 @@ import {
   OpenAIEmbeddingsProvider,
   WorkspaceIndexer,
   loadConfigFile
-} from "./chunk-GGL3XTMV.js";
+} from "./chunk-ENM3P2PS.js";
 
 // src/cli.ts
 import yargs from "yargs";

package/dist/index.cjs

@@ -2325,8 +2325,8 @@ var Neo4jGraphStore = class {
         const stmts = [
           `CREATE CONSTRAINT ${Repo}_repo_id IF NOT EXISTS FOR (r:${Repo}) REQUIRE r.repo_id IS UNIQUE`,
           `CREATE CONSTRAINT ${Symbol2}_id IF NOT EXISTS FOR (s:${Symbol2}) REQUIRE s.id IS UNIQUE`,
-          `CREATE CONSTRAINT ${External}_key IF NOT EXISTS FOR (e:${External}) REQUIRE (e.repo_id, e.kind, e.value) IS NODE KEY`,
-          `CREATE CONSTRAINT ${File}_key IF NOT EXISTS FOR (f:${File}) REQUIRE (f.repo_id, f.path) IS NODE KEY`
+          `CREATE CONSTRAINT ${External}_key IF NOT EXISTS FOR (e:${External}) REQUIRE e.key IS UNIQUE`,
+          `CREATE CONSTRAINT ${File}_key IF NOT EXISTS FOR (f:${File}) REQUIRE f.key IS UNIQUE`
         ];
         for (const q of stmts) {
           try {
@@ -2452,10 +2452,18 @@ var Neo4jGraphStore = class {
       await s.run(
         `MERGE (r:${Repo} {repo_id:$repoId})
          SET r.repo_root=$repoRoot, r.commit=$commit, r.branch=$branch, r.updated_at=timestamp()
-         MERGE (f:${File} {repo_id:$repoId, path:$path})
-         SET f.repo_root=$repoRoot, f.language=$language, f.updated_at=timestamp()
+         MERGE (f:${File} {key:$fileKey})
+         SET f.repo_id=$repoId, f.path=$path, f.repo_root=$repoRoot, f.language=$language, f.updated_at=timestamp()
          MERGE (r)-[:HAS_FILE]->(f)`,
-        { repoId: update.repoId, repoRoot: update.repoRoot, commit: update.commit, branch: update.branch, path: update.path, language: update.language }
+        {
+          repoId: update.repoId,
+          repoRoot: update.repoRoot,
+          commit: update.commit,
+          branch: update.branch,
+          path: update.path,
+          language: update.language,
+          fileKey: `${update.repoId}:${update.path}`
+        }
       );
       const fileEdges = [
         ...update.imports.map((v) => ({ kind: "import", value: v })),
@@ -2465,9 +2473,14 @@ var Neo4jGraphStore = class {
       await s.run(
         `MATCH (f:${File} {repo_id:$repoId, path:$path})
          UNWIND $edges AS e
-         MERGE (x:${External} {repo_id:$repoId, kind:e.kind, value:e.value})
+         MERGE (x:${External} {key:e.key})
+         SET x.repo_id=$repoId, x.kind=e.kind, x.value=e.value
          MERGE (f)-[:FILE_EDGE {kind:e.kind}]->(x)`,
-        { repoId: update.repoId, path: update.path, edges: fileEdges }
+        {
+          repoId: update.repoId,
+          path: update.path,
+          edges: fileEdges.map((e) => ({ ...e, key: `${update.repoId}:${e.kind}:${e.value}` }))
+        }
       ).catch(() => void 0);
       await s.run(
         `MATCH (f:${File} {repo_id:$repoId, path:$path})-[r:FILE_EDGE]->(x:${External})
@@ -3395,6 +3408,16 @@ var RepoFileIndexer = class {
       return;
     }
     this.emit({ type: "repo/index/file/start", repoRoot: this.repoRoot, path: posixRelPath });
+    const stage = (stageName, stageStartedAt) => {
+      this.emit({
+        type: "repo/index/file/stage",
+        repoRoot: this.repoRoot,
+        path: posixRelPath,
+        stage: stageName,
+        ms: Date.now() - stageStartedAt
+      });
+    };
+    const readStartedAt = Date.now();
     const abs = import_node_path14.default.join(this.repoRoot, fromPosixPath(posixRelPath));
     let stat;
     try {
@@ -3418,16 +3441,20 @@ var RepoFileIndexer = class {
     }
     const raw = buf.toString("utf8");
     const redacted = this.applyRedactions(raw);
+    stage("read", readStartedAt);
     const fileHash = sha256Hex(redacted);
     const prev = this.store.getFileHash(posixRelPath);
     if (prev === fileHash) {
       this.emit({ type: "repo/index/file/skip", repoRoot: this.repoRoot, path: posixRelPath, reason: "unchanged" });
       return;
     }
+    const chunkStartedAt = Date.now();
     const { language, chunks } = chunkSource(posixRelPath, redacted, this.config.chunk);
+    stage("chunk", chunkStartedAt);
     let imports = [];
     let exports2 = [];
     if (language === "typescript" || language === "javascript") {
+      const relationsStartedAt = Date.now();
       const rel = extractTsRelations(posixRelPath, redacted);
       imports = rel.imports;
       exports2 = rel.exports;
@@ -3435,12 +3462,14 @@ var RepoFileIndexer = class {
       this.store.setEdges(posixRelPath, "export", rel.exports);
       this.workspaceStore?.setEdges(this.repoId, posixRelPath, "import", rel.imports);
       this.workspaceStore?.setEdges(this.repoId, posixRelPath, "export", rel.exports);
+      stage("relations", relationsStartedAt);
     } else {
       this.store.setEdges(posixRelPath, "import", []);
       this.store.setEdges(posixRelPath, "export", []);
       this.workspaceStore?.setEdges(this.repoId, posixRelPath, "import", []);
       this.workspaceStore?.setEdges(this.repoId, posixRelPath, "export", []);
     }
+    const synopsisStartedAt = Date.now();
     const synopsisText = buildSynopsis(posixRelPath, language, redacted);
     const synopsis = synopsisText.trim() ? [
       {
@@ -3465,14 +3494,18 @@ var RepoFileIndexer = class {
       }
     ] : [];
     const combined = [...synopsis, ...headerChunk, ...chunks.map((c) => ({ ...c, kind: "chunk" }))];
+    stage("synopsis", synopsisStartedAt);
+    const embedStartedAt = Date.now();
     const embedTexts = [];
     const embedPlan = [];
     const embeddings = combined.map(() => null);
+    let cached2 = 0;
     for (let i = 0; i < combined.length; i++) {
       const ch = combined[i];
-      const cached2 = this.embeddingCache.get(this.embedder.id, ch.contentHash);
-      if (cached2) {
-        embeddings[i] = cached2;
+      const cachedEmb = this.embeddingCache.get(this.embedder.id, ch.contentHash);
+      if (cachedEmb) {
+        embeddings[i] = cachedEmb;
+        cached2++;
         continue;
       }
       embedTexts.push(
@@ -3504,11 +3537,22 @@ ${ch.text}`
         this.embeddingCache.put(this.embedder.id, plan.contentHash, vecs[j]);
       }
     }
+    this.emit({
+      type: "repo/index/file/embed/done",
+      repoRoot: this.repoRoot,
+      path: posixRelPath,
+      chunks: combined.length,
+      cached: cached2,
+      computed: embedTexts.length,
+      ms: Date.now() - embedStartedAt
+    });
+    stage("embed", embedStartedAt);
     const fileMtime = stat.mtimeMs;
     const ftsMode = this.config.storage.ftsMode;
     const storeText = this.config.storage.storeText;
     const oldChunkIds = this.store.listChunksForFile(posixRelPath).map((r) => r.id);
     const points = [];
+    const storeStartedAt = Date.now();
     const rows = combined.map((ch, i) => {
       const id = sha256Hex(
         `${this.repoId}:${posixRelPath}:${ch.kind}:${ch.startLine}:${ch.endLine}:${ch.contentHash}`
@@ -3536,7 +3580,19 @@ ${ch.text}`
     this.store.replaceChunksForFile(posixRelPath, rows);
     this.workspaceStore?.upsertFile(this.repoId, posixRelPath, fileHash, fileMtime, language, stat.size);
     this.workspaceStore?.replaceChunksForFile(this.repoId, this.repoRoot, posixRelPath, rows);
+    stage("store", storeStartedAt);
+    const symbolsStartedAt = Date.now();
     const symbolOut = await this.indexSymbolsIfEnabled(posixRelPath, language, redacted, fileHash);
+    this.emit({
+      type: "repo/index/file/symbols",
+      repoRoot: this.repoRoot,
+      path: posixRelPath,
+      symbols: symbolOut?.symbols?.length ?? 0,
+      edges: symbolOut?.edges?.length ?? 0,
+      ms: Date.now() - symbolsStartedAt
+    });
+    stage("symbols", symbolsStartedAt);
+    const graphStartedAt = Date.now();
     const head = this.getHead();
     if (this.graphStore && head) {
       await this.graphStore.replaceFileGraph({
@@ -3552,7 +3608,10 @@ ${ch.text}`
         symbolEdges: (symbolOut?.edges ?? []).map((e) => ({ fromId: e.fromId, toId: e.toId, kind: e.kind }))
       }).catch(() => void 0);
     }
+    stage("graph", graphStartedAt);
+    const vectorStartedAt = Date.now();
     await this.ensureVectorUpToDate(points, oldChunkIds);
+    stage("vector", vectorStartedAt);
     this.emit({
       type: "repo/index/file/done",
       repoRoot: this.repoRoot,
@@ -4163,11 +4222,14 @@ var RepoIndexer = class {
     const uniq3 = Array.from(new Set(posixPaths)).slice(0, maxFiles);
     for (const p of uniq3) {
       if (opts?.signal?.aborted) return;
+      const startedAt = Date.now();
+      this.emitProgress({ type: "repo/symbolGraph/expand/start", repoRoot: this.repoRoot, path: p });
       const abs = import_node_path17.default.join(this.repoRoot, p.split("/").join(import_node_path17.default.sep));
       let text = "";
       try {
         text = import_node_fs12.default.readFileSync(abs, "utf8");
       } catch {
+        this.emitProgress({ type: "repo/symbolGraph/expand/done", repoRoot: this.repoRoot, path: p, edges: 0, ms: Date.now() - startedAt });
         continue;
       }
       const contentHash = this.store.getFileHash(p) ?? void 0;
@@ -4185,6 +4247,7 @@ var RepoIndexer = class {
         fromPath: p,
         edges: normalized.map((e) => ({ fromId: e.fromId, toId: e.toId, kind: e.kind, toPath: e.toPath }))
       }).catch(() => void 0);
+      this.emitProgress({ type: "repo/symbolGraph/expand/done", repoRoot: this.repoRoot, path: p, edges: normalized.length, ms: Date.now() - startedAt });
     }
   }
   async watch() {
@@ -4771,11 +4834,14 @@ var WorkspaceIndexer = class {
           if (seeds.length >= 4) break;
         }
         if (seeds.length > 0) {
+          const gs = Date.now();
+          this.emitProgress({ type: "workspace/retrieve/graph/start", workspaceRoot: this.workspaceRoot, seeds: seeds.length });
           graphNeighborFiles = await this.graphStore.neighborFiles({
             seeds,
             limit: profile.name === "architecture" ? 16 : 10,
             kinds: ["definition", "reference", "implementation", "typeDefinition"]
           });
+          this.emitProgress({ type: "workspace/retrieve/graph/done", workspaceRoot: this.workspaceRoot, neighbors: graphNeighborFiles.length, ms: Date.now() - gs });
         }
       }
     } catch {

package/dist/index.d.cts

@@ -253,6 +253,15 @@ type IndexerProgressEvent = {
         lexical: number;
         merged: number;
     };
+} | {
+    type: "workspace/retrieve/graph/start";
+    workspaceRoot: string;
+    seeds: number;
+} | {
+    type: "workspace/retrieve/graph/done";
+    workspaceRoot: string;
+    ms: number;
+    neighbors: number;
 } | {
     type: "repo/open";
     repoRoot: string;
@@ -267,11 +276,32 @@ type IndexerProgressEvent = {
     type: "repo/index/file/start";
     repoRoot: string;
     path: string;
+} | {
+    type: "repo/index/file/stage";
+    repoRoot: string;
+    path: string;
+    stage: "read" | "chunk" | "relations" | "synopsis" | "embed" | "store" | "symbols" | "graph" | "vector";
+    ms?: number;
 } | {
     type: "repo/index/file/skip";
     repoRoot: string;
     path: string;
     reason: string;
+} | {
+    type: "repo/index/file/embed/done";
+    repoRoot: string;
+    path: string;
+    chunks: number;
+    cached: number;
+    computed: number;
+    ms: number;
+} | {
+    type: "repo/index/file/symbols";
+    repoRoot: string;
+    path: string;
+    symbols: number;
+    edges: number;
+    ms: number;
 } | {
     type: "repo/index/file/done";
     repoRoot: string;
@@ -306,6 +336,16 @@ type IndexerProgressEvent = {
     type: "repo/vector/flush";
     repoRoot: string;
     kind: string;
+} | {
+    type: "repo/symbolGraph/expand/start";
+    repoRoot: string;
+    path: string;
+} | {
+    type: "repo/symbolGraph/expand/done";
+    repoRoot: string;
+    path: string;
+    edges: number;
+    ms: number;
 } | {
     type: "repo/watch/start";
     repoRoot: string;

package/dist/index.d.ts

@@ -253,6 +253,15 @@ type IndexerProgressEvent = {
         lexical: number;
         merged: number;
     };
+} | {
+    type: "workspace/retrieve/graph/start";
+    workspaceRoot: string;
+    seeds: number;
+} | {
+    type: "workspace/retrieve/graph/done";
+    workspaceRoot: string;
+    ms: number;
+    neighbors: number;
 } | {
     type: "repo/open";
     repoRoot: string;
@@ -267,11 +276,32 @@ type IndexerProgressEvent = {
     type: "repo/index/file/start";
     repoRoot: string;
     path: string;
+} | {
+    type: "repo/index/file/stage";
+    repoRoot: string;
+    path: string;
+    stage: "read" | "chunk" | "relations" | "synopsis" | "embed" | "store" | "symbols" | "graph" | "vector";
+    ms?: number;
 } | {
     type: "repo/index/file/skip";
     repoRoot: string;
     path: string;
     reason: string;
+} | {
+    type: "repo/index/file/embed/done";
+    repoRoot: string;
+    path: string;
+    chunks: number;
+    cached: number;
+    computed: number;
+    ms: number;
+} | {
+    type: "repo/index/file/symbols";
+    repoRoot: string;
+    path: string;
+    symbols: number;
+    edges: number;
+    ms: number;
 } | {
     type: "repo/index/file/done";
     repoRoot: string;
@@ -306,6 +336,16 @@ type IndexerProgressEvent = {
     type: "repo/vector/flush";
     repoRoot: string;
     kind: string;
+} | {
+    type: "repo/symbolGraph/expand/start";
+    repoRoot: string;
+    path: string;
+} | {
+    type: "repo/symbolGraph/expand/done";
+    repoRoot: string;
+    path: string;
+    edges: number;
+    ms: number;
 } | {
     type: "repo/watch/start";
     repoRoot: string;

package/dist/index.js

@@ -27,7 +27,7 @@ import {
   mergeIndexerConfig,
   pickRepoOverride,
   stableSymbolId
-} from "./chunk-GGL3XTMV.js";
+} from "./chunk-ENM3P2PS.js";
 
 // src/symbolGraph/vscodeProvider.ts
 import path2 from "path";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@neuralsea/workspace-indexer",
-  "version": "0.3.2",
+  "version": "0.3.4",
   "description": "Local-first multi-repo workspace indexer (semantic embeddings + git-aware incremental updates + hybrid retrieval profiles) for AI agents.",
   "type": "module",
   "main": "./dist/index.cjs",