trace-mcp 1.6.1 → 1.7.0

package/dist/cli.js

@@ -530,8 +530,8 @@ var require_utils = __commonJS({
       }
       return output;
     };
-    exports.basename = (path107, { windows } = {}) => {
-      const segs = path107.split(windows ? /[\\/]/ : "/");
+    exports.basename = (path108, { windows } = {}) => {
+      const segs = path108.split(windows ? /[\\/]/ : "/");
       const last = segs[segs.length - 1];
       if (last === "") {
         return segs[segs.length - 2];
@@ -1960,7 +1960,7 @@ var require_picomatch = __commonJS({
     };
     picomatch3.isMatch = (str2, patterns, options) => picomatch3(patterns, options)(str2);
     picomatch3.parse = (pattern, options) => {
-      if (Array.isArray(pattern)) return pattern.map((p4) => picomatch3.parse(p4, options));
+      if (Array.isArray(pattern)) return pattern.map((p5) => picomatch3.parse(p5, options));
       return parse(pattern, { ...options, fastpaths: false });
     };
     picomatch3.scan = (input, options) => scan(input, options);
@@ -2083,7 +2083,7 @@ function detectLayerPreset(store) {
     let matchCount = 0;
     for (const layer of layers) {
       const hasMatch = layer.path_prefixes.some(
-        (prefix) => paths.some((p4) => p4.startsWith(prefix))
+        (prefix) => paths.some((p5) => p5.startsWith(prefix))
       );
       if (hasMatch) matchCount++;
     }
@@ -2115,9 +2115,9 @@ var init_layer_violations = __esm({
 });
 
 // src/cli.ts
-import { Command as Command10 } from "commander";
-import path106 from "path";
-import fs94 from "fs";
+import { Command as Command12 } from "commander";
+import path107 from "path";
+import fs96 from "fs";
 import { randomUUID } from "crypto";
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
 import { StreamableHTTPServerTransport } from "@modelcontextprotocol/sdk/server/streamableHttp.js";
@@ -2134,7 +2134,7 @@ var logger = pino({
 }, process.stderr);
 
 // src/db/schema.ts
-var SCHEMA_VERSION = 16;
+var SCHEMA_VERSION = 17;
 var DDL = `
 -- ============================================================
 -- UNIFIED ADDRESS SPACE
@@ -3015,6 +3015,25 @@ var MIGRATIONS = {
         AND (json_extract(metadata, '$.extends') IS NOT NULL
           OR json_extract(metadata, '$.implements') IS NOT NULL)
     `);
+  },
+  17: (db) => {
+    db.exec(`
+      CREATE TABLE IF NOT EXISTS indexing_progress (
+        pipeline TEXT PRIMARY KEY,
+        phase TEXT NOT NULL DEFAULT 'idle',
+        processed INTEGER NOT NULL DEFAULT 0,
+        total INTEGER NOT NULL DEFAULT 0,
+        started_at INTEGER NOT NULL DEFAULT 0,
+        completed_at INTEGER NOT NULL DEFAULT 0,
+        error TEXT,
+        updated_at INTEGER NOT NULL DEFAULT 0
+      )
+    `);
+    db.exec(`
+      INSERT OR IGNORE INTO indexing_progress (pipeline) VALUES ('indexing');
+      INSERT OR IGNORE INTO indexing_progress (pipeline) VALUES ('summarization');
+      INSERT OR IGNORE INTO indexing_progress (pipeline) VALUES ('embedding');
+    `);
   }
 };
 function runMigrations(db, fromVersion) {
@@ -3129,14 +3148,14 @@ var FileRepository = class {
   }
   db;
   _stmts;
-  insertFile(path107, language, contentHash, byteLength, workspace, mtimeMs, createNode) {
-    const result = this._stmts.insertFile.run(path107, language, contentHash, byteLength, workspace, mtimeMs);
+  insertFile(path108, language, contentHash, byteLength, workspace, mtimeMs, createNode) {
+    const result = this._stmts.insertFile.run(path108, language, contentHash, byteLength, workspace, mtimeMs);
     const fileId = Number(result.lastInsertRowid);
     createNode("file", fileId);
     return fileId;
   }
-  getFile(path107) {
-    return this._stmts.getFile.get(path107);
+  getFile(path108) {
+    return this._stmts.getFile.get(path108);
   }
   getFileById(id) {
     return this._stmts.getFileById.get(id);
@@ -3366,6 +3385,24 @@ var SymbolRepository = class {
   updateSymbolSummary(symbolId, summary) {
     this.db.prepare("UPDATE symbols SET summary = ? WHERE id = ?").run(summary, symbolId);
   }
+  countUnsummarizedSymbols(kinds) {
+    if (kinds.length === 0) return 0;
+    const placeholders = kinds.map(() => "?").join(",");
+    const row = this.db.prepare(`
+      SELECT COUNT(*) as cnt FROM symbols s
+      JOIN files f ON s.file_id = f.id
+      WHERE s.summary IS NULL AND s.kind IN (${placeholders}) AND f.gitignored = 0
+    `).get(...kinds);
+    return row.cnt;
+  }
+  countUnembeddedSymbols() {
+    const row = this.db.prepare(`
+      SELECT COUNT(*) as cnt FROM symbols s
+      LEFT JOIN symbol_embeddings se ON se.symbol_id = s.id
+      WHERE se.symbol_id IS NULL
+    `).get();
+    return row.cnt;
+  }
   getUnsummarizedSymbols(kinds, limit) {
     if (kinds.length === 0) return [];
     const placeholders = kinds.map(() => "?").join(",");
@@ -3980,9 +4017,9 @@ var Store = class {
   domain;
   analytics;
   // --- Files (delegates to FileRepository) ---
-  insertFile(path107, language, contentHash, byteLength, workspace, mtimeMs) {
+  insertFile(path108, language, contentHash, byteLength, workspace, mtimeMs) {
     return this.files.insertFile(
-      path107,
+      path108,
       language,
       contentHash,
       byteLength,
@@ -3991,8 +4028,8 @@ var Store = class {
       (nodeType, refId) => this.graph.createNode(nodeType, refId)
     );
   }
-  getFile(path107) {
-    return this.files.getFile(path107);
+  getFile(path108) {
+    return this.files.getFile(path108);
   }
   getFileById(id) {
     return this.files.getFileById(id);
@@ -4080,6 +4117,12 @@ var Store = class {
   updateSymbolSummary(symbolId, summary) {
     this.symbols.updateSymbolSummary(symbolId, summary);
   }
+  countUnsummarizedSymbols(kinds) {
+    return this.symbols.countUnsummarizedSymbols(kinds);
+  }
+  countUnembeddedSymbols() {
+    return this.symbols.countUnembeddedSymbols();
+  }
   getUnsummarizedSymbols(kinds, limit) {
     return this.symbols.getUnsummarizedSymbols(kinds, limit);
   }
@@ -4264,7 +4307,7 @@ var PluginRegistry = class {
   }
   getActiveFrameworkPlugins(ctx) {
     if (this._activeFrameworkCache) return this._activeFrameworkCache;
-    const active = this.frameworkPlugins.filter((p4) => p4.detect(ctx));
+    const active = this.frameworkPlugins.filter((p5) => p5.detect(ctx));
     this._activeFrameworkCache = this.topologicalSort(active);
     return this._activeFrameworkCache;
   }
@@ -4295,8 +4338,8 @@ var PluginRegistry = class {
   }
   topologicalSort(plugins) {
     const nameMap = /* @__PURE__ */ new Map();
-    for (const p4 of plugins) {
-      nameMap.set(p4.manifest.name, p4);
+    for (const p5 of plugins) {
+      nameMap.set(p5.manifest.name, p5);
     }
     const sorted = [];
     const visited = /* @__PURE__ */ new Set();
@@ -4346,8 +4389,170 @@ var GLOBAL_CONFIG_PATH = path.join(TRACE_MCP_HOME, ".config.json");
 var INDEX_DIR = path.join(TRACE_MCP_HOME, "index");
 var REGISTRY_PATH = path.join(TRACE_MCP_HOME, "registry.json");
 var TOPOLOGY_DB_PATH = path.join(TRACE_MCP_HOME, "topology.db");
+function stripJsonComments(text) {
+  let result = "";
+  let i = 0;
+  while (i < text.length) {
+    if (text[i] === '"') {
+      const start = i;
+      i++;
+      while (i < text.length && text[i] !== '"') {
+        if (text[i] === "\\") i++;
+        i++;
+      }
+      i++;
+      result += text.slice(start, i);
+      continue;
+    }
+    if (text[i] === "/" && text[i + 1] === "/") {
+      while (i < text.length && text[i] !== "\n") i++;
+      continue;
+    }
+    result += text[i];
+    i++;
+  }
+  return result.replace(/,(\s*[}\]])/g, "$1");
+}
+var DEFAULT_CONFIG_JSONC = `{
+  // \u2500\u2500 AI / Embeddings \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500
+  "ai": {
+    "enabled": false,
+    "provider": "ollama",                       // "ollama" | "openai"
+    // "base_url": "http://localhost:11434",     // custom endpoint
+    // "api_key": "",                            // required for openai; or set OPENAI_API_KEY env
+    // "inference_model": "",                    // ollama: "gemma4-e4b", openai: "gpt-4o-mini"
+    // "fast_model": "",                         // ollama: "gemma4-e4b", openai: "gpt-4o-mini"
+    // "embedding_model": "",                    // ollama: "qwen3-embedding:0.6b", openai: "text-embedding-3-small"
+    // "embedding_dimensions": 1536,             // provider-specific
+    "summarize_on_index": true,
+    "summarize_batch_size": 20,
+    "summarize_kinds": ["class", "function", "method", "interface", "trait", "enum", "type"],
+    "concurrency": 1                            // match OLLAMA_NUM_PARALLEL for ollama
+    // "reranker_model": ""                      // optional: e.g. "bge-reranker-v2-m3"
+  },
+
+  // \u2500\u2500 Security \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500
+  "security": {
+    // "secret_patterns": [],                    // extra regex patterns to detect secrets
+    // "max_file_size_bytes": 1048576,           // skip files larger than this (1 MB)
+    // "max_files": 10000                        // max files per project
+  },
+
+  // \u2500\u2500 Predictive analysis \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500
+  "predictive": {
+    "enabled": true,
+    "weights": {
+      "bug":         { "churn": 0.20, "fix_ratio": 0.20, "complexity": 0.20, "coupling": 0.15, "pagerank": 0.10, "authors": 0.15 },
+      "tech_debt":   { "complexity": 0.30, "coupling": 0.25, "test_gap": 0.25, "churn": 0.20 },
+      "change_risk": { "blast_radius": 0.25, "complexity": 0.20, "churn": 0.20, "test_gap": 0.20, "coupling": 0.15 }
+    },
+    "cache_ttl_minutes": 60,
+    "git_since_days": 180,
+    "module_depth": 2
+  },
+
+  // \u2500\u2500 Intent / domain classification \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500
+  "intent": {
+    "enabled": false,
+    // "domain_hints": {},                       // { "domain_name": ["path/pattern/**"] }
+    // "custom_domains": [],                     // [{ "name": "...", "path_patterns": ["..."] }]
+    "auto_classify_on_index": true,
+    "classify_batch_size": 100
+  },
+
+  // \u2500\u2500 Runtime tracing (OpenTelemetry) \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500
+  "runtime": {
+    "enabled": false,
+    "otlp": {
+      "port": 4318,
+      "host": "127.0.0.1",
+      "max_body_bytes": 4194304
+    },
+    "retention": {
+      "max_span_age_days": 7,
+      "max_aggregate_age_days": 90,
+      "prune_interval": 100
+    },
+    "mapping": {
+      "fqn_attributes": ["code.function", "code.namespace", "code.filepath"],
+      "route_patterns": ["^(?:GET|POST|PUT|PATCH|DELETE|HEAD|OPTIONS)\\\\s+(.+)$"]
+    }
+  },
+
+  // \u2500\u2500 Cross-repo topology \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500
+  "topology": {
+    "enabled": true,
+    // "repos": [],                              // extra repo paths to federate
+    "auto_detect": true,
+    "auto_federation": true
+    // "contract_globs": []                      // globs for API contract files
+  },
+
+  // \u2500\u2500 Quality gates \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500
+  "quality_gates": {
+    "enabled": true,
+    "fail_on": "error",                          // "error" | "warning" | "none"
+    "rules": {
+      // "max_cyclomatic_complexity":       { "threshold": 20, "severity": "error" },
+      // "max_coupling_instability":        { "threshold": 0.8, "severity": "warning" },
+      // "max_circular_import_chains":      { "threshold": 0, "severity": "error" },
+      // "max_dead_exports_percent":        { "threshold": 10, "severity": "warning" },
+      // "max_tech_debt_grade":             { "threshold": "C", "severity": "warning" },
+      // "max_security_critical_findings":  { "threshold": 0, "severity": "error" },
+      // "max_antipattern_count":           { "threshold": 5, "severity": "warning" },
+      // "max_code_smell_count":            { "threshold": 10, "severity": "warning" }
+    }
+  },
+
+  // \u2500\u2500 Tool exposure \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500
+  "tools": {
+    "preset": "full",                            // "full" | "minimal" | custom preset name
+    // "include": [],                            // whitelist specific tools
+    // "exclude": [],                            // blacklist specific tools
+    // "descriptions": {},                       // override tool descriptions
+    "description_verbosity": "full",             // "full" | "minimal" | "none"
+    "instructions_verbosity": "full",            // "full" | "minimal" | "none"
+    "meta_fields": true                          // true | false | ["_hints", "_budget_warning", ...]
+  },
+
+  // \u2500\u2500 Indexing ignore rules \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500
+  "ignore": {
+    "directories": [],                           // extra directory names to skip
+    "patterns": []                               // extra gitignore-style patterns
+  },
+
+  // \u2500\u2500 Framework-specific \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500
+  "frameworks": {
+    "laravel": {
+      "artisan": { "enabled": true, "timeout": 10000 },
+      "graceful_degradation": true
+    }
+  },
+
+  // \u2500\u2500 File watcher \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500
+  "watch": {
+    "enabled": true,
+    "debounceMs": 2000
+  },
+
+  // \u2500\u2500 Per-project overrides \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500
+  // Keys are absolute paths; values override any top-level setting for that project.
+  // Example:
+  // "projects": {
+  //   "/path/to/project": {
+  //     "ai": { "enabled": true, "concurrency": 4 },
+  //     "include": ["src/**/*.ts"],
+  //     "exclude": ["dist/**"]
+  //   }
+  // }
+  "projects": {}
+}
+`;
 function ensureGlobalDirs() {
   fs.mkdirSync(INDEX_DIR, { recursive: true });
+  if (!fs.existsSync(GLOBAL_CONFIG_PATH)) {
+    fs.writeFileSync(GLOBAL_CONFIG_PATH, DEFAULT_CONFIG_JSONC);
+  }
 }
 function projectHash(absolutePath) {
   return crypto.createHash("sha256").update(absolutePath).digest("hex").slice(0, 12);
@@ -4569,7 +4774,7 @@ var TraceMcpConfigSchema = z.object({
 function loadGlobalConfigRaw() {
   if (!fs2.existsSync(GLOBAL_CONFIG_PATH)) return {};
   try {
-    return JSON.parse(fs2.readFileSync(GLOBAL_CONFIG_PATH, "utf-8"));
+    return JSON.parse(stripJsonComments(fs2.readFileSync(GLOBAL_CONFIG_PATH, "utf-8")));
   } catch {
     return {};
   }
@@ -5947,7 +6152,7 @@ function extractSymbolSource(content, symbolName, symbolKind) {
   }
   let startLine = -1;
   for (let i = 0; i < lines.length; i++) {
-    if (patterns.some((p4) => p4.test(lines[i]))) {
+    if (patterns.some((p5) => p5.test(lines[i]))) {
       startLine = i;
       break;
     }
@@ -7409,16 +7614,18 @@ var EnvIndexer = class {
 
 // src/indexer/pipeline.ts
 var IndexingPipeline = class _IndexingPipeline {
-  constructor(store, registry, config, rootPath) {
+  constructor(store, registry, config, rootPath, progress) {
     this.store = store;
     this.registry = registry;
     this.config = config;
     this.rootPath = rootPath;
+    this.progress = progress;
   }
   store;
   registry;
   config;
   rootPath;
+  progress;
   workspaces = [];
   _lock = Promise.resolve();
   _projectContext;
@@ -7503,6 +7710,13 @@ var IndexingPipeline = class _IndexingPipeline {
       errors: 0,
       durationMs: 0
     };
+    this.progress?.update("indexing", {
+      phase: "running",
+      processed: 0,
+      total: relPaths.length,
+      startedAt: Date.now(),
+      completedAt: 0
+    });
     this._projectContext = void 0;
     this.registry.clearCaches();
     this._changedFileIds.clear();
@@ -7549,6 +7763,8 @@ var IndexingPipeline = class _IndexingPipeline {
           persister.persistBatch(extractions);
           result.indexed += extractions.length;
         }
+        const processed = result.indexed + result.skipped + result.errors;
+        this.progress?.update("indexing", { processed });
       }
       enableFts5Triggers(this.store.db);
       const edgeResolver = new EdgeResolver(this.getPipelineState());
@@ -7574,6 +7790,11 @@ var IndexingPipeline = class _IndexingPipeline {
     }
     result.durationMs = Date.now() - startMs;
     result.incremental = this._isIncremental;
+    this.progress?.update("indexing", {
+      phase: "completed",
+      processed: result.indexed + result.skipped + result.errors,
+      completedAt: Date.now()
+    });
     logger.info(result, "Indexing pipeline completed");
     return result;
   }
@@ -8169,14 +8390,16 @@ async function hybridSearch(db, query, vectorStore, embeddingService, limit, rer
 // src/ai/embedding-pipeline.ts
 var DEFAULT_BATCH_SIZE = 50;
 var EmbeddingPipeline = class {
-  constructor(store, embeddingService, vectorStore) {
+  constructor(store, embeddingService, vectorStore, progress) {
     this.store = store;
     this.embeddingService = embeddingService;
     this.vectorStore = vectorStore;
+    this.progress = progress;
   }
   store;
   embeddingService;
   vectorStore;
+  progress;
   async indexSymbol(symbolId, text) {
     const embedding = await this.embeddingService.embed(text);
     if (embedding.length > 0) {
@@ -8184,10 +8407,48 @@ var EmbeddingPipeline = class {
     }
   }
   /**
-   * Find symbols that don't have embeddings yet and embed them.
-   * Returns the number of newly embedded symbols.
+   * Find symbols that don't have embeddings yet and embed them in a loop.
+   * Reports progress and returns the total number of newly embedded symbols.
    */
   async indexUnembedded(batchSize = DEFAULT_BATCH_SIZE) {
+    const totalToEmbed = this.store.countUnembeddedSymbols();
+    if (totalToEmbed === 0) return 0;
+    this.progress?.update("embedding", {
+      phase: "running",
+      processed: 0,
+      total: totalToEmbed,
+      startedAt: Date.now(),
+      completedAt: 0
+    });
+    let totalIndexed = 0;
+    try {
+      let batch;
+      do {
+        batch = await this.embedBatch(batchSize);
+        totalIndexed += batch;
+        if (batch > 0) {
+          this.progress?.update("embedding", { processed: totalIndexed });
+        }
+      } while (batch > 0);
+      this.progress?.update("embedding", {
+        phase: "completed",
+        processed: totalIndexed,
+        completedAt: Date.now()
+      });
+    } catch (e) {
+      this.progress?.update("embedding", {
+        phase: "error",
+        error: e instanceof Error ? e.message : String(e)
+      });
+      throw e;
+    }
+    return totalIndexed;
+  }
+  /**
+   * Embed a single batch of unembedded symbols.
+   * Returns the number of symbols embedded in this batch.
+   */
+  async embedBatch(batchSize) {
     const unembedded = this.store.db.prepare(`
       SELECT s.id, s.name, s.fqn, s.kind, s.signature, s.summary
       FROM symbols s
@@ -8218,13 +8479,7 @@ var EmbeddingPipeline = class {
    */
   async reindexAll() {
     this.store.db.exec("DELETE FROM symbol_embeddings");
-    let total = 0;
-    let batch;
-    do {
-      batch = await this.indexUnembedded(DEFAULT_BATCH_SIZE);
-      total += batch;
-    } while (batch > 0);
-    return total;
+    return this.indexUnembedded(DEFAULT_BATCH_SIZE);
   }
 };
 function buildEmbeddingText(symbol) {
@@ -8406,31 +8661,53 @@ import fs12 from "fs";
 import path12 from "path";
 var MAX_SOURCE_LINES = 80;
 var SummarizationPipeline = class {
-  constructor(store, inferenceService, rootPath, config) {
+  constructor(store, inferenceService, rootPath, config, progress) {
     this.store = store;
     this.inferenceService = inferenceService;
     this.rootPath = rootPath;
     this.config = config;
+    this.progress = progress;
   }
   store;
   inferenceService;
   rootPath;
   config;
+  progress;
   async summarizeUnsummarized() {
     let totalSummarized = 0;
     let batch;
-    do {
-      batch = this.store.getUnsummarizedSymbols(this.config.kinds, this.config.batchSize);
-      if (batch.length === 0) break;
-      const results = await this.summarizeBatch(batch);
-      for (const { id, summary } of results) {
-        this.store.updateSymbolSummary(id, summary);
-        totalSummarized++;
-      }
-      logger.debug({ batch: batch.length, total: totalSummarized }, "Summarization batch complete");
-    } while (batch.length === this.config.batchSize);
-    if (totalSummarized > 0) {
-      logger.info({ totalSummarized }, "Symbol summarization complete");
+    const total = this.store.countUnsummarizedSymbols(this.config.kinds);
+    if (total === 0) return 0;
+    this.progress?.update("summarization", {
+      phase: "running",
+      processed: 0,
+      total,
+      startedAt: Date.now(),
+      completedAt: 0
+    });
+    try {
+      do {
+        batch = this.store.getUnsummarizedSymbols(this.config.kinds, this.config.batchSize);
+        if (batch.length === 0) break;
+        const results = await this.summarizeBatch(batch);
+        for (const { id, summary } of results) {
+          this.store.updateSymbolSummary(id, summary);
+          totalSummarized++;
+        }
+        this.progress?.update("summarization", { processed: totalSummarized });
+        logger.debug({ batch: batch.length, total: totalSummarized }, "Summarization batch complete");
+      } while (batch.length === this.config.batchSize);
+      this.progress?.update("summarization", {
+        phase: "completed",
+        processed: totalSummarized,
+        completedAt: Date.now()
+      });
+    } catch (e) {
+      this.progress?.update("summarization", {
+        phase: "error",
+        error: e instanceof Error ? e.message : String(e)
+      });
+      throw e;
     }
     return totalSummarized;
   }
@@ -9232,8 +9509,8 @@ var SessionJournal = class _SessionJournal {
     };
     this.entries.push(entry);
     if (tool === "get_symbol" || tool === "get_outline") {
-      const path107 = params.path ?? params.file_path ?? "";
-      if (path107) this.filesRead.add(path107);
+      const path108 = params.path ?? params.file_path ?? "";
+      if (path108) this.filesRead.add(path108);
     }
     if (resultCount === 0 && this.isSearchTool(tool)) {
       this.zeroResultQueries.set(hash, summary);
@@ -9389,7 +9666,7 @@ var SessionJournal = class _SessionJournal {
         fileReads.set(file, existing);
       }
     }
-    const focusFiles = [...fileReads.entries()].sort((a, b) => b[1].reads - a[1].reads).slice(0, maxFiles).map(([p4, v]) => ({ path: p4, reads: v.reads, last_tool: v.lastTool }));
+    const focusFiles = [...fileReads.entries()].sort((a, b) => b[1].reads - a[1].reads).slice(0, maxFiles).map(([p5, v]) => ({ path: p5, reads: v.reads, last_tool: v.lastTool }));
     const editedSet = /* @__PURE__ */ new Set();
     for (const entry of this.entries) {
       if (entry.tool === "register_edit") {
@@ -10020,7 +10297,7 @@ function getIndexHealth(store, config) {
 }
 function getProjectMap(store, registry, summaryOnly, projectContext) {
   const stats = store.getStats();
-  const frameworks = registry.getAllFrameworkPlugins().map((p4) => p4.manifest.name);
+  const frameworks = registry.getAllFrameworkPlugins().map((p5) => p5.manifest.name);
   const detectedVersions = projectContext?.detectedVersions;
   if (summaryOnly) {
     const languageRows2 = store.db.prepare(
@@ -10133,7 +10410,7 @@ var W_KIND = 0.15;
 var W_SIGNATURE = 0.25;
 var W_TOKEN = 0.15;
 function tokenizeName(name) {
-  const parts = name.replace(/([a-z])([A-Z])/g, "$1_$2").toLowerCase().split(/[_\-./:]+/).filter((p4) => p4.length > 1);
+  const parts = name.replace(/([a-z])([A-Z])/g, "$1_$2").toLowerCase().split(/[_\-./:]+/).filter((p5) => p5.length > 1);
   return new Set(parts);
 }
 function jaccard(a, b) {
@@ -10304,10 +10581,13 @@ function registerCoreTools(server, ctx) {
   const { store, registry, config, projectRoot, guardPath, j: j3, jh, journal } = ctx;
   server.tool(
     "get_index_health",
-    "Get index status, statistics, and health information",
+    "Get index status, statistics, health information, and pipeline progress (indexing, summarization, embedding)",
     {},
     async () => {
       const result = getIndexHealth(store, config);
+      if (ctx.progress) {
+        result.progress = ctx.progress.snapshot();
+      }
       return { content: [{ type: "text", text: j3(result) }] };
     }
   );
@@ -10699,8 +10979,8 @@ function getCoChangesForFile(store, filePath, graphFiles) {
 function findAffectedTests(store, targetPath, dependentPaths) {
   const seen = /* @__PURE__ */ new Set();
   const allPaths = [targetPath, ...dependentPaths];
-  for (const p4 of allPaths) {
-    const file = store.getFile(p4);
+  for (const p5 of allPaths) {
+    const file = store.getFile(p5);
     if (!file) continue;
     const fileNodeId = store.getNodeId("file", file.id);
     if (fileNodeId != null) {
@@ -10998,9 +11278,9 @@ function deduplicateByFile(rawDeps) {
     }
   }
   const result = [];
-  for (const [path107, entry] of fileMap) {
+  for (const [path108, entry] of fileMap) {
     const dep = {
-      path: path107,
+      path: path108,
       edgeTypes: [...entry.edgeTypes],
       depth: entry.depth
     };
@@ -11582,7 +11862,7 @@ function getContextBundle(store, rootPath, opts) {
     }
     primarySymbols.push({ sym, file });
   }
-  const primaryInternalIds = primarySymbols.map((p4) => p4.sym.id);
+  const primaryInternalIds = primarySymbols.map((p5) => p5.sym.id);
   const primaryNodeMap = store.getNodeIdsBatch("symbol", primaryInternalIds);
   const primaryNodeIds = primaryInternalIds.map((id) => primaryNodeMap.get(id)).filter((n) => n != null);
   const seenDepIds = new Set(primaryInternalIds);
@@ -11657,7 +11937,7 @@ function getContextBundle(store, rootPath, opts) {
     }
   }
   const primaryItems = primarySymbols.map(
-    (p4, i) => toContextItem(p4.sym, p4.file, rootPath, 1 - i * 0.01)
+    (p5, i) => toContextItem(p5.sym, p5.file, rootPath, 1 - i * 0.01)
   );
   const depItems = depSymbols.map(
     (d, i) => toContextItem(d.sym, d.file, rootPath, 0.8 - i * 5e-3)
@@ -11673,7 +11953,7 @@ function getContextBundle(store, rootPath, opts) {
     totalBudget: budget
   });
   const result = {
-    primary: primarySymbols.map((p4) => toBundleItem(p4.sym, p4.file)),
+    primary: primarySymbols.map((p5) => toBundleItem(p5.sym, p5.file)),
     dependencies: depSymbols.slice(0, assembled.dependencies.length).map((d) => toBundleItem(d.sym, d.file)),
     callers: callerSymbols.slice(0, assembled.callers.length).map((c) => toBundleItem(c.sym, c.file)),
     totalTokens: assembled.totalTokens,
@@ -12096,7 +12376,7 @@ function suggestQueries(store) {
 // src/tools/navigation/related.ts
 import { ok as ok4, err as err5 } from "neverthrow";
 function tokenizeName2(name) {
-  const parts = name.replace(/([a-z])([A-Z])/g, "$1_$2").toLowerCase().split(/[_\-.]/).filter((p4) => p4.length > 1);
+  const parts = name.replace(/([a-z])([A-Z])/g, "$1_$2").toLowerCase().split(/[_\-.]/).filter((p5) => p5.length > 1);
   return new Set(parts);
 }
 function jaccard2(a, b) {
@@ -13470,8 +13750,8 @@ var NestJSPlugin = class {
       const patterns = extractMicroservicePatterns(source);
       if (patterns.length > 0) {
         if (!result.routes) result.routes = [];
-        for (const p4 of patterns) {
-          result.routes.push({ method: p4.type === "message" ? "MSG" : "EVT", uri: p4.pattern });
+        for (const p5 of patterns) {
+          result.routes.push({ method: p5.type === "message" ? "MSG" : "EVT", uri: p5.pattern });
         }
       }
     }
@@ -14381,8 +14661,8 @@ function getLivewireContext(store, componentName) {
   const properties = [];
   const actions = [];
   if (Array.isArray(meta.properties)) {
-    for (const p4 of meta.properties) {
-      properties.push({ name: String(p4.name ?? ""), type: p4.type });
+    for (const p5 of meta.properties) {
+      properties.push({ name: String(p5.name ?? ""), type: p5.type });
     }
   }
   if (Array.isArray(meta.actions)) {
@@ -15026,18 +15306,18 @@ function getApiSurface(store, filePattern) {
   };
 }
 function getPluginRegistry(store, registry, activeFrameworkNames) {
-  const languagePlugins = registry.getLanguagePlugins().map((p4) => ({
-    name: p4.manifest.name,
-    version: p4.manifest.version,
-    priority: p4.manifest.priority,
-    extensions: p4.supportedExtensions
+  const languagePlugins = registry.getLanguagePlugins().map((p5) => ({
+    name: p5.manifest.name,
+    version: p5.manifest.version,
+    priority: p5.manifest.priority,
+    extensions: p5.supportedExtensions
   }));
-  const frameworkPlugins = registry.getAllFrameworkPlugins().map((p4) => ({
-    name: p4.manifest.name,
-    version: p4.manifest.version,
-    priority: p4.manifest.priority,
-    dependencies: p4.manifest.dependencies ?? [],
-    active: activeFrameworkNames.has(p4.manifest.name)
+  const frameworkPlugins = registry.getAllFrameworkPlugins().map((p5) => ({
+    name: p5.manifest.name,
+    version: p5.manifest.version,
+    priority: p5.manifest.priority,
+    dependencies: p5.manifest.dependencies ?? [],
+    active: activeFrameworkNames.has(p5.manifest.name)
   }));
   const edgeTypes = store.getEdgeTypes();
   return {
@@ -15580,7 +15860,7 @@ function getComplexityTrend(store, cwd, filePath, options = {}) {
 function registerAnalysisTools(server, ctx) {
   const { store, registry, projectRoot, guardPath, j: j3, jh } = ctx;
   const frameworkNames = new Set(
-    registry.getAllFrameworkPlugins().map((p4) => p4.manifest.name)
+    registry.getAllFrameworkPlugins().map((p5) => p5.manifest.name)
   );
   server.tool(
     "get_implementations",
@@ -15890,7 +16170,7 @@ var BARREL_PATTERNS = [
 ];
 function isBarrelFile(filePath) {
   const base = path30.basename(filePath);
-  return BARREL_PATTERNS.some((p4) => p4.test(base));
+  return BARREL_PATTERNS.some((p5) => p5.test(base));
 }
 function buildImportedNamesSet(store) {
   const importedNames = /* @__PURE__ */ new Set();
@@ -17057,7 +17337,7 @@ function detectEmptyFunctions(content, lines, symbols, filePath, language) {
     const strippedLines = body.split("\n").map((l) => l.trim()).filter((l) => l.length > 0).filter((l) => !/^(?:\/\/|#|--|\/\*|\*\/|\*)\s*$/.test(l));
     const joined = strippedLines.join("\n");
     const isEmpty = strippedLines.length === 0;
-    const isStub = !isEmpty && strippedLines.length <= 2 && STUB_BODY_PATTERNS.some((p4) => p4.test(joined));
+    const isStub = !isEmpty && strippedLines.length <= 2 && STUB_BODY_PATTERNS.some((p5) => p5.test(joined));
     if (isEmpty || isStub) {
       const description = isEmpty ? `Empty ${sym.kind} '${sym.name}' \u2014 no implementation` : `Stub ${sym.kind} '${sym.name}' \u2014 placeholder implementation`;
       findings.push({
@@ -17189,8 +17469,8 @@ function detectHardcodedValues(lines, filePath) {
   return findings;
 }
 var PRIORITY_ORDER = { high: 0, medium: 1, low: 2 };
-function priorityRank(p4) {
-  return PRIORITY_ORDER[p4];
+function priorityRank(p5) {
+  return PRIORITY_ORDER[p5];
 }
 var BATCH_SIZE2 = 100;
 var MAX_FILE_SIZE2 = 512 * 1024;
@@ -17659,8 +17939,8 @@ function interProceduralAnalysis(store, projectRoot, perFileResults, limit) {
         const sig = sym.signature ?? "";
         const paramMatch = sig.match(/\(([^)]*)\)/);
         if (paramMatch) {
-          const params = paramMatch[1].split(",").map((p4) => {
-            const trimmed = p4.trim();
+          const params = paramMatch[1].split(",").map((p5) => {
+            const trimmed = p5.trim();
             const parts = trimmed.split(/[\s:]+/);
             return parts[0].replace(/^[&*$]/, "").trim();
           });
@@ -17698,7 +17978,7 @@ function taintAnalysis(store, projectRoot, opts = {}) {
   const sinkFilter = opts.sinks ? new Set(opts.sinks) : null;
   const scope = opts.scope?.replace(/\/+$/, "");
   const files = scope ? store.db.prepare("SELECT path, language FROM files WHERE path LIKE ? AND (status = 'ok' OR status IS NULL)").all(`${scope}%`) : store.db.prepare("SELECT path, language FROM files WHERE (status = 'ok' OR status IS NULL)").all();
-  const isTest = (p4) => /(?:^|\/)(?:tests?|__tests__|spec)\/|\.(?:test|spec)\.\w+$/.test(p4);
+  const isTest = (p5) => /(?:^|\/)(?:tests?|__tests__|spec)\/|\.(?:test|spec)\.\w+$/.test(p5);
   const sourceFiles = files.filter((f) => !isTest(f.path) && f.language);
   let allFlows = [];
   let analyzed = 0;
@@ -19221,7 +19501,7 @@ ${bodyLines.join("\n")}`;
       callSite = `${baseIndent}${functionName}(${paramStr})`;
     }
   } else if (lang === "go") {
-    const paramStr = params.map((p4) => `${p4} interface{}`).join(", ");
+    const paramStr = params.map((p5) => `${p5} interface{}`).join(", ");
     const returnTypes = returns.length > 0 ? ` (${returns.map(() => "interface{}").join(", ")})` : "";
     functionDef = `func ${functionName}(${paramStr})${returnTypes} {
 ${bodyLines.join("\n")}`;
@@ -19842,7 +20122,7 @@ CREATE INDEX IF NOT EXISTS idx_client_calls_target ON client_calls(target_repo_i
 CREATE INDEX IF NOT EXISTS idx_client_calls_endpoint ON client_calls(matched_endpoint_id);
 `;
 function findBestEndpointMatch(urlPattern, method, endpoints) {
-  const normalize = (p4) => p4.replace(/\{[^}]+\}/g, "{*}").replace(/:[\w]+/g, "{*}").replace(/\/+$/, "");
+  const normalize = (p5) => p5.replace(/\{[^}]+\}/g, "{*}").replace(/:[\w]+/g, "{*}").replace(/\/+$/, "");
   const normalizedUrl = normalize(urlPattern);
   let bestMatch = null;
   let bestScore = 0;
@@ -20216,9 +20496,9 @@ function detectFromDockerCompose(root) {
   const composeFiles = ["docker-compose.yml", "docker-compose.yaml", "compose.yml", "compose.yaml"];
   let composePath;
   for (const f of composeFiles) {
-    const p4 = path36.join(root, f);
-    if (fs25.existsSync(p4)) {
-      composePath = p4;
+    const p5 = path36.join(root, f);
+    if (fs25.existsSync(p5)) {
+      composePath = p5;
       break;
     }
   }
@@ -21692,9 +21972,9 @@ var RuntimeAggregator = class {
     return { bucketsUpdated: rows.length, nodesAffected: nodesAffected.size };
   }
 };
-function percentile(sorted, p4) {
+function percentile(sorted, p5) {
   if (sorted.length === 0) return 0;
-  const idx = Math.ceil(p4 * sorted.length) - 1;
+  const idx = Math.ceil(p5 * sorted.length) - 1;
   return sorted[Math.max(0, idx)];
 }
 
@@ -21706,7 +21986,7 @@ var RuntimeIntelligence = class {
     this.ingester = new SpanIngester(store.db, config.retention.prune_interval);
     this.mapper = new SpanMapper(store, {
       fqnAttributes: config.mapping.fqn_attributes,
-      routePatterns: config.mapping.route_patterns.map((p4) => new RegExp(p4))
+      routePatterns: config.mapping.route_patterns.map((p5) => new RegExp(p5))
     });
     this.aggregator = new RuntimeAggregator(store.db);
   }
@@ -22889,16 +23169,16 @@ function findShortestPath(store, startNodeId, endNodeId, maxDepth) {
         parent.set(nodeId, { from, edgeType: edge.edge_type_name });
         nextFrontier.push(nodeId);
         if (nodeId === endNodeId) {
-          const path107 = [endNodeId];
+          const path108 = [endNodeId];
           const edgeTypes = [];
           let cur = endNodeId;
           while (cur !== startNodeId) {
-            const p4 = parent.get(cur);
-            path107.unshift(p4.from);
-            edgeTypes.unshift(p4.edgeType);
-            cur = p4.from;
+            const p5 = parent.get(cur);
+            path108.unshift(p5.from);
+            edgeTypes.unshift(p5.edgeType);
+            cur = p5.from;
           }
-          return { path: path107, edgeTypes };
+          return { path: path108, edgeTypes };
         }
       }
     }
@@ -22920,7 +23200,7 @@ function generateMermaid(nodes, edges, paths) {
     lines.push(`  ${id}["${label}"]`);
   }
   if (paths && paths.length > 0) {
-    const pathSymbols = new Set(paths.flatMap((p4) => p4.map((s) => s.symbol_id)));
+    const pathSymbols = new Set(paths.flatMap((p5) => p5.map((s) => s.symbol_id)));
     const pathIds = [...pathSymbols].map((sid) => idMap.get(sid)).filter(Boolean);
     if (pathIds.length > 0) {
       lines.push(`  style ${pathIds.join(",")} fill:#f9f,stroke:#333,stroke-width:2px`);
@@ -23182,7 +23462,7 @@ function getDataflow(store, projectRoot, opts) {
     const retMatch = line.match(/\breturn\s+(.+?)(?:;|\s*$)/);
     if (retMatch) {
       const expr = retMatch[1].trim();
-      const sources = params.map((p4) => p4.name).filter((name) => new RegExp(`\\b${escapeRegex3(name)}\\b`).test(expr));
+      const sources = params.map((p5) => p5.name).filter((name) => new RegExp(`\\b${escapeRegex3(name)}\\b`).test(expr));
       returns.push({ expression: expr, line: absLine, sources });
     }
   }
@@ -23193,7 +23473,7 @@ function getDataflow(store, projectRoot, opts) {
     const assignMatch = line.match(/(?:const|let|var)\s+(\w+)\s*=\s*(.+?)(?:;|\s*$)/);
     if (assignMatch) {
       const [, varName, source] = assignMatch;
-      const involvesParam = params.some((p4) => new RegExp(`\\b${escapeRegex3(p4.name)}\\b`).test(source));
+      const involvesParam = params.some((p5) => new RegExp(`\\b${escapeRegex3(p5.name)}\\b`).test(source));
       if (involvesParam || /\w+\s*\(/.test(source)) {
         localAssignments.push({
           name: varName,
@@ -23220,15 +23500,15 @@ function parseParameters(signature) {
   if (!match) return [];
   const paramStr = match[1].trim();
   if (!paramStr) return [];
-  return paramStr.split(",").map((p4) => {
-    const trimmed = p4.trim();
+  return paramStr.split(",").map((p5) => {
+    const trimmed = p5.trim();
     const tsMatch = trimmed.match(/^(\w+)\??\s*:\s*(.+)$/);
     if (tsMatch) return { name: tsMatch[1], type: tsMatch[2].trim() };
     const pyMatch = trimmed.match(/^(\w+)(?:\s*:\s*(.+))?$/);
     if (pyMatch) return { name: pyMatch[1], type: pyMatch[2]?.trim() ?? null };
     const word = trimmed.split(/\s/)[0];
     return { name: word, type: null };
-  }).filter((p4) => p4.name && p4.name !== "...");
+  }).filter((p5) => p5.name && p5.name !== "...");
 }
 function buildCalleeMap(store, symbol) {
   const map = /* @__PURE__ */ new Map();
@@ -23859,7 +24139,7 @@ function predictBugs(store, cwd, options = {}) {
   const couplingMap = /* @__PURE__ */ new Map();
   for (const c of couplingResults) couplingMap.set(c.file, c);
   const pagerankMap = /* @__PURE__ */ new Map();
-  for (const p4 of pagerankResults) pagerankMap.set(p4.file, p4);
+  for (const p5 of pagerankResults) pagerankMap.set(p5.file, p5);
   const complexityRows = store.db.prepare(`
     SELECT f.path, MAX(s.cyclomatic) as max_cyclomatic
     FROM symbols s JOIN files f ON s.file_id = f.id
@@ -25365,7 +25645,7 @@ function autoLabel(files) {
   const segments = /* @__PURE__ */ new Map();
   const ignore = /* @__PURE__ */ new Set(["src", "lib", "app", "dist", "build", "node_modules", "vendor", "index"]);
   for (const file of files) {
-    const parts = file.split("/").filter((p4) => !ignore.has(p4) && !p4.includes("."));
+    const parts = file.split("/").filter((p5) => !ignore.has(p5) && !p5.includes("."));
     for (const part of parts) {
       segments.set(part, (segments.get(part) ?? 0) + 1);
     }
@@ -26099,8 +26379,8 @@ function getPackageDeps(options) {
     const manifest = readManifest(absPath);
     repoManifests.set(repoPath, manifest);
     const allPublishes = [...entry.publishes ?? [], ...manifest.publishes];
-    for (const p4 of new Set(allPublishes)) {
-      publishMap.set(p4, { repo: entry.name ?? path44.basename(repoPath), repoPath });
+    for (const p5 of new Set(allPublishes)) {
+      publishMap.set(p5, { repo: entry.name ?? path44.basename(repoPath), repoPath });
     }
   }
   const results = [];
@@ -26111,8 +26391,8 @@ function getPackageDeps(options) {
     for (const [repoPath, manifest] of repoManifests) {
       const entry = registry[repoPath];
       if (entry?.name === project || path44.basename(repoPath) === project) {
-        for (const p4 of manifest.publishes) {
-          targetPackages.add(p4);
+        for (const p5 of manifest.publishes) {
+          targetPackages.add(p5);
         }
       }
     }
@@ -26149,7 +26429,7 @@ function getPackageDeps(options) {
     for (const [repoPath, manifest] of repoManifests) {
       const entry = registry[repoPath];
       const repoName = entry?.name ?? path44.basename(repoPath);
-      const isTarget = manifest.publishes.some((p4) => targetPackages.has(p4));
+      const isTarget = manifest.publishes.some((p5) => targetPackages.has(p5));
       if (!isTarget && targetPackages.size > 0) continue;
       for (const [dep, info] of manifest.deps) {
         const publisher = publishMap.get(dep);
@@ -26685,10 +26965,10 @@ function getScopeFiles(store, scope, scopePath, query, limit) {
 function buildFileTree(paths) {
   const lines = [];
   const sorted = paths.sort();
-  for (const p4 of sorted.slice(0, 200)) {
-    const depth = p4.split("/").length - 1;
+  for (const p5 of sorted.slice(0, 200)) {
+    const depth = p5.split("/").length - 1;
     const indent = "  ".repeat(Math.min(depth, 6));
-    lines.push(`${indent}${path45.basename(p4)}`);
+    lines.push(`${indent}${path45.basename(p5)}`);
   }
   if (sorted.length > 200) {
     lines.push(`  ... and ${sorted.length - 200} more files`);
@@ -27462,10 +27742,10 @@ function getManifestPath() {
   return path47.join(BUNDLES_DIR, "manifest.json");
 }
 function loadManifest() {
-  const p4 = getManifestPath();
-  if (!fs35.existsSync(p4)) return { bundles: [] };
+  const p5 = getManifestPath();
+  if (!fs35.existsSync(p5)) return { bundles: [] };
   try {
-    return JSON.parse(fs35.readFileSync(p4, "utf-8"));
+    return JSON.parse(fs35.readFileSync(p5, "utf-8"));
   } catch {
     return { bundles: [] };
   }
@@ -27761,8 +28041,8 @@ var AnalyticsStore = class {
   db;
   constructor(dbPath) {
     ensureGlobalDirs();
-    const p4 = dbPath ?? ANALYTICS_DB_PATH;
-    this.db = new Database5(p4);
+    const p5 = dbPath ?? ANALYTICS_DB_PATH;
+    this.db = new Database5(p5);
     this.db.pragma("journal_mode = WAL");
     this.db.pragma("foreign_keys = OFF");
     this.db.exec(SCHEMA_SQL);
@@ -28751,6 +29031,94 @@ function benchmarkTaskContext(store, symbols, files, count, rand) {
   });
   return buildScenario("composite_task", "NL task \u2192 optimal code context (baseline: search + read 5-8 files + grep)", details);
 }
+function benchmarkFindUsages(store, symbols, count, rand) {
+  const sampled = sample(symbols.filter((s) => s.kind === "function" || s.kind === "method"), count, rand);
+  const details = sampled.map((s) => {
+    const grepMatches = 10;
+    const grepContextLines = 5;
+    const grepChars = grepMatches * grepContextLines * 80;
+    const bl = estimateTokens3(grepChars);
+    const tm = estimateTokens3(grepMatches * 60);
+    return { query: s.name, file: s.file_path, baseline_tokens: bl, trace_mcp_tokens: tm, reduction_pct: reductionPct(bl, tm) };
+  });
+  return buildScenario("find_usages", "All usages of a symbol (baseline: grep with context lines)", details);
+}
+function benchmarkContextBundle(store, symbols, count, rand) {
+  const funcs = symbols.filter((s) => s.kind === "function" || s.kind === "method");
+  const batchSize = 3;
+  const batches = Math.min(count, Math.floor(funcs.length / batchSize));
+  const sampled = sample(funcs, batches * batchSize, rand);
+  const details = [];
+  for (let i = 0; i < batches; i++) {
+    const group = sampled.slice(i * batchSize, (i + 1) * batchSize);
+    const totalSourceBytes = group.reduce((s, sym) => s + (sym.source_bytes || Math.round(sym.file_byte_length * 0.08)), 0);
+    const importOverhead = group.length * 200;
+    const bl = estimateTokens3(totalSourceBytes + importOverhead);
+    const tm = estimateTokens3(Math.round((totalSourceBytes + importOverhead) * 0.6));
+    const names = group.map((g) => g.name).join(", ");
+    details.push({ query: names, file: group[0].file_path, baseline_tokens: bl, trace_mcp_tokens: tm, reduction_pct: reductionPct(bl, tm) });
+  }
+  return buildScenario("context_bundle", "Batch symbol+imports lookup (baseline: N \xD7 get_symbol + Read imports)", details);
+}
+function benchmarkBatchOverhead(symbols, files, count, rand) {
+  const batchSize = 3;
+  const batches = Math.min(count, Math.floor(symbols.length / batchSize));
+  const sampledSymbols = sample(symbols, batches * batchSize, rand);
+  const details = [];
+  for (let i = 0; i < batches; i++) {
+    const group = sampledSymbols.slice(i * batchSize, (i + 1) * batchSize);
+    const perCallOverhead = 150;
+    const contentTokens = group.reduce((s, sym) => s + estimateTokens3(sym.source_bytes || 200), 0);
+    const bl = contentTokens + batchSize * perCallOverhead;
+    const tm = contentTokens + perCallOverhead;
+    const names = group.map((g) => g.name).join(", ");
+    details.push({ query: names, file: group[0].file_path, baseline_tokens: bl, trace_mcp_tokens: tm, reduction_pct: reductionPct(bl, tm) });
+  }
+  return buildScenario("batch_overhead", "N independent queries batched (baseline: N separate MCP round-trips)", details);
+}
+function benchmarkTypeHierarchy(store, symbols, count, rand) {
+  const types = symbols.filter((s) => s.kind === "interface" || s.kind === "class");
+  const sampled = sample(types, count, rand);
+  const details = sampled.map((s) => {
+    const nodeRow = store.db.prepare(
+      "SELECT n.id FROM nodes n JOIN symbols sym ON n.ref_id = sym.id AND n.node_type = ? WHERE sym.symbol_id = ?"
+    ).get("symbol", s.symbol_id);
+    let implFileBytes = 0;
+    let implCount = 0;
+    if (nodeRow) {
+      const impls = store.db.prepare(`
+        SELECT DISTINCT f.byte_length FROM edges e
+        JOIN edge_types et ON e.edge_type_id = et.id
+        JOIN nodes n2 ON e.source_node_id = n2.id AND n2.node_type = 'symbol'
+        JOIN symbols s2 ON n2.ref_id = s2.id
+        JOIN files f ON s2.file_id = f.id
+        WHERE e.target_node_id = ?
+          AND et.name IN ('implements', 'extends')
+        LIMIT 10
+      `).all(nodeRow.id);
+      implFileBytes = impls.reduce((sum, d) => sum + (d.byte_length || 0), 0);
+      implCount = impls.length;
+    }
+    const grepChars = Math.max(implCount, 3) * 5 * 80;
+    const readChars = implFileBytes || s.file_byte_length * 3;
+    const bl = estimateTokens3(grepChars + readChars);
+    const tm = estimateTokens3(Math.max(implCount, 3) * 120);
+    return { query: s.name, file: s.file_path, baseline_tokens: bl, trace_mcp_tokens: tm, reduction_pct: reductionPct(bl, tm) };
+  });
+  return buildScenario("type_hierarchy", "Find all implementations of interface/class (baseline: grep + read files)", details);
+}
+function benchmarkTestsFor(store, symbols, count, rand) {
+  const sampled = sample(symbols.filter((s) => s.kind === "function" || s.kind === "method"), count, rand);
+  const details = sampled.map((s) => {
+    const globTokens = 200;
+    const grepTokens = 3 * 5 * 80 / 3.5;
+    const testFileReadTokens = 2 * estimateTokens3(3e3);
+    const bl = Math.round(globTokens + grepTokens + testFileReadTokens);
+    const tm = estimateTokens3(400);
+    return { query: s.name, file: s.file_path, baseline_tokens: bl, trace_mcp_tokens: tm, reduction_pct: reductionPct(bl, tm) };
+  });
+  return buildScenario("tests_for", "Find tests for a symbol (baseline: glob + grep + read test files)", details);
+}
 function runBenchmark(store, opts = {}) {
   const n = opts.queries ?? 10;
   const rand = seededRandom(opts.seed ?? 42);
@@ -28760,8 +29128,13 @@ function runBenchmark(store, opts = {}) {
     benchmarkSymbolLookup(symbols, n, rand),
     benchmarkFileExploration(files, n, rand),
     benchmarkSearch(symbols, n, rand),
+    benchmarkFindUsages(store, symbols, n, rand),
+    benchmarkContextBundle(store, symbols, n, rand),
+    benchmarkBatchOverhead(symbols, files, n, rand),
     benchmarkImpactAnalysis(store, symbols, n, rand),
     benchmarkCallGraph(store, symbols, n, rand),
+    benchmarkTypeHierarchy(store, symbols, n, rand),
+    benchmarkTestsFor(store, symbols, n, rand),
     benchmarkTaskContext(store, symbols, files, n, rand)
   ];
   const totalQueries = scenarios.reduce((s, sc) => s + sc.queries, 0);
@@ -29329,11 +29702,11 @@ function registerPrompts(server, ctx) {
           sections.push("");
         }
       }
-      const deadCode = safe2(() => getDeadCodeV2(store, { threshold: 0.5, limit: 10 }), { items: [] });
-      if (deadCode.items && deadCode.items.length > 0) {
-        sections.push(`## Dead Code Candidates (${deadCode.items.length})
+      const deadCode = safe2(() => getDeadCodeV2(store, { threshold: 0.5, limit: 10 }), { dead_symbols: [], file_pattern: null, total_exports: 0, total_dead: 0, threshold: 0.5 });
+      if (deadCode.dead_symbols && deadCode.dead_symbols.length > 0) {
+        sections.push(`## Dead Code Candidates (${deadCode.dead_symbols.length})
 `);
-        for (const d of deadCode.items.slice(0, 5)) {
+        for (const d of deadCode.dead_symbols.slice(0, 5)) {
           sections.push(`- ${d.name} in ${d.file} (confidence: ${d.confidence})`);
         }
         sections.push("");
@@ -29372,10 +29745,10 @@ Provide a thorough code review with risk assessment, suggested tests, and archit
       sections.push("```json");
       sections.push(JSON.stringify(map, null, 2));
       sections.push("```\n");
-      const health = safe2(() => getRepoHealth(store), {});
+      const health = safe2(() => getRepoHealth(store), null);
       sections.push("## Architecture Health\n");
-      sections.push(`- Coupling metrics: ${health.coupling_summary?.total ?? "N/A"} files analyzed`);
-      sections.push(`- Dependency cycles: ${health.cycles?.length ?? 0}`);
+      sections.push(`- Files in graph: ${health?.summary?.files_in_graph ?? "N/A"}`);
+      sections.push(`- Dependency cycles: ${health?.cycles?.length ?? 0}`);
       sections.push("");
       sections.push("## Key Entry Points\n");
       const context = safe2(() => getFeatureContext(store, projectRoot, "main entry point application startup", 4e3), { symbols: [] });
@@ -29458,7 +29831,7 @@ Analyze this bug. Identify the most likely failure point, suggest debugging step
       sections.push(`## Dependency Cycles: ${cycles.length}
 `);
       for (const c of cycles.slice(0, 5)) {
-        sections.push(`- ${c.join(" \u2192 ")}`);
+        sections.push(`- ${c.files.join(" \u2192 ")}`);
       }
       sections.push("");
       const debt = safe2(() => getTechDebt(store, projectRoot, {
@@ -29539,11 +29912,11 @@ Analyze this project's architecture health. Identify the most critical issues an
         sections.push(...riskFiles);
         sections.push("");
       }
-      const dead = safe2(() => getDeadCodeV2(store, { threshold: 0.6, limit: 10 }), { items: [] });
-      if (dead.items && dead.items.length > 0) {
-        sections.push(`## Potential Dead Code: ${dead.items.length}
+      const dead = safe2(() => getDeadCodeV2(store, { threshold: 0.6, limit: 10 }), { dead_symbols: [], file_pattern: null, total_exports: 0, total_dead: 0, threshold: 0.6 });
+      if (dead.dead_symbols && dead.dead_symbols.length > 0) {
+        sections.push(`## Potential Dead Code: ${dead.dead_symbols.length}
 `);
-        for (const d of dead.items.slice(0, 5)) {
+        for (const d of dead.dead_symbols.slice(0, 5)) {
           sections.push(`- ${d.name} (${d.file})`);
         }
         sections.push("");
@@ -29884,7 +30257,7 @@ function registerSessionTools(server, ctx) {
 }
 
 // src/server/server.ts
-var PKG_VERSION = true ? "1.6.1" : "0.0.0-dev";
+var PKG_VERSION = true ? "1.7.0" : "0.0.0-dev";
 function j2(value) {
   return JSON.stringify(value, (_key, val) => val === null || val === void 0 ? void 0 : val);
 }
@@ -29988,10 +30361,10 @@ function extractCompactResult(toolName, response) {
     return void 0;
   }
 }
-function createServer2(store, registry, config, rootPath) {
+function createServer2(store, registry, config, rootPath, progress) {
   const projectRoot = rootPath ?? process.cwd();
   const frameworkNames = new Set(
-    registry.getAllFrameworkPlugins().map((p4) => p4.manifest.name)
+    registry.getAllFrameworkPlugins().map((p5) => p5.manifest.name)
   );
   const has = (...names) => names.some((n) => frameworkNames.has(n));
   const detectedFrameworks = [...frameworkNames].join(", ") || "none";
@@ -30097,7 +30470,7 @@ function createServer2(store, registry, config, rootPath) {
   const embeddingService = config.ai?.enabled ? aiProvider.embedding() : null;
   const reranker = config.ai?.enabled ? new LLMReranker(aiProvider.fastInference()) : null;
   if (config.watch?.enabled !== false) {
-    const knownExtensions = new Set(registry.getLanguagePlugins().flatMap((p4) => p4.supportedExtensions));
+    const knownExtensions = new Set(registry.getLanguagePlugins().flatMap((p5) => p5.supportedExtensions));
     const fileWatcher = new FileWatcher(
       projectRoot,
       async (files) => {
@@ -30135,7 +30508,8 @@ function createServer2(store, registry, config, rootPath) {
     guardPath,
     j: j2,
     jh,
-    markExplored: explored.markExplored
+    markExplored: explored.markExplored,
+    progress: progress ?? null
   };
   const metaCtx = {
     ...ctx,
@@ -31535,8 +31909,8 @@ function extractProps(scriptContent) {
     const body = typeMatch[1];
     const propNames = body.match(/(\w+)\s*[?]?\s*:/g);
     if (propNames) {
-      for (const p4 of propNames) {
-        props.push(p4.replace(/\s*[?]?\s*:/, ""));
+      for (const p5 of propNames) {
+        props.push(p5.replace(/\s*[?]?\s*:/, ""));
       }
     }
     return props;
@@ -31556,8 +31930,8 @@ function extractProps(scriptContent) {
     const body = objectMatch[1];
     const propNames = body.match(/(\w+)\s*:/g);
     if (propNames) {
-      for (const p4 of propNames) {
-        const name = p4.replace(/\s*:/, "");
+      for (const p5 of propNames) {
+        const name = p5.replace(/\s*:/, "");
         if (!["type", "default", "required", "validator"].includes(name)) {
           props.push(name);
         }
@@ -31692,7 +32066,7 @@ var VueLanguagePlugin = class {
         kind: "component",
         framework: "vue",
         ...props.length > 0 && {
-          props: Object.fromEntries(props.map((p4) => [p4, { type: "unknown" }]))
+          props: Object.fromEntries(props.map((p5) => [p5, { type: "unknown" }]))
         },
         ...emits.length > 0 && { emits },
         ...composables.length > 0 && { composables }
@@ -34281,9 +34655,9 @@ function extractImplMethods(body, filePath, typeName, typeSymbolId) {
       if (isPublic(child)) meta.exported = 1;
       const params = child.childForFieldName("parameters");
       if (params) {
-        for (const p4 of params.namedChildren) {
-          if (p4.type === "self_parameter") {
-            meta.receiver = p4.text;
+        for (const p5 of params.namedChildren) {
+          if (p5.type === "self_parameter") {
+            meta.receiver = p5.text;
             break;
           }
         }
@@ -36575,7 +36949,7 @@ var ObjCLanguagePlugin = class {
       const selectorLine = m[2].trim();
       const parts = selectorLine.match(/\w+(?=\s*:)|^\w+$/gm);
       if (!parts) continue;
-      const selector = parts.length === 1 && !selectorLine.includes(":") ? parts[0] : parts.map((p4) => p4 + ":").join("");
+      const selector = parts.length === 1 && !selectorLine.includes(":") ? parts[0] : parts.map((p5) => p5 + ":").join("");
       const isStatic = prefix === "+";
       add(selector, "method", m.index, m[0], { static: isStatic });
     }
@@ -38675,9 +39049,9 @@ var XmlLanguagePlugin = class {
       }
       const schemaLoc = getAttr(attrs, "schemaLocation");
       if (schemaLoc) {
-        for (const p4 of schemaLoc.trim().split(/\s+/)) {
-          if (p4.endsWith(".xsd") || p4.endsWith(".wsdl") || p4.startsWith("http")) {
-            edges.push({ edgeType: "imports", metadata: { module: p4, tag } });
+        for (const p5 of schemaLoc.trim().split(/\s+/)) {
+          if (p5.endsWith(".xsd") || p5.endsWith(".wsdl") || p5.startsWith("http")) {
+            edges.push({ edgeType: "imports", metadata: { module: p5, tag } });
           }
         }
       }
@@ -38741,7 +39115,7 @@ var PrismaPlugin = class {
         path51.join(ctx.rootPath, "prisma", "schema.prisma"),
         path51.join(ctx.rootPath, "schema.prisma")
       ];
-      return candidates.some((p4) => fs38.existsSync(p4));
+      return candidates.some((p5) => fs38.existsSync(p5));
     } catch {
       return false;
     }
@@ -38812,7 +39186,7 @@ function parsePrismaSchema(source) {
       const fieldName = fieldMatch[1];
       const fieldType = fieldMatch[2];
       const attrs = fieldMatch[3] ?? "";
-      if (["@@", "//"].some((p4) => fieldName.startsWith(p4))) continue;
+      if (["@@", "//"].some((p5) => fieldName.startsWith(p5))) continue;
       const field = {
         name: fieldName,
         type: fieldType.replace("?", "").replace("[]", ""),
@@ -40197,7 +40571,7 @@ import { ok as ok32 } from "neverthrow";
 function symId3(filePath, name, kind) {
   return `${filePath}::${name}#${kind}`;
 }
-function stripJsonComments(source) {
+function stripJsonComments2(source) {
   let result = "";
   let i = 0;
   let inString = false;
@@ -40316,8 +40690,8 @@ function extractEslint(obj, add, edges) {
     }
   }
   if (Array.isArray(obj.plugins)) {
-    for (const p4 of obj.plugins) {
-      if (typeof p4 === "string") edges.push({ edgeType: "imports", metadata: { module: p4, dialect: "eslint" } });
+    for (const p5 of obj.plugins) {
+      if (typeof p5 === "string") edges.push({ edgeType: "imports", metadata: { module: p5, dialect: "eslint" } });
     }
   }
 }
@@ -40347,14 +40721,14 @@ function extractLerna(obj, add) {
 }
 function extractBabel(obj, add, edges) {
   if (Array.isArray(obj.presets)) {
-    for (const p4 of obj.presets) {
-      const name = typeof p4 === "string" ? p4 : Array.isArray(p4) && typeof p4[0] === "string" ? p4[0] : null;
+    for (const p5 of obj.presets) {
+      const name = typeof p5 === "string" ? p5 : Array.isArray(p5) && typeof p5[0] === "string" ? p5[0] : null;
       if (name) edges.push({ edgeType: "imports", metadata: { module: name, dialect: "babel" } });
     }
   }
   if (Array.isArray(obj.plugins)) {
-    for (const p4 of obj.plugins) {
-      const name = typeof p4 === "string" ? p4 : Array.isArray(p4) && typeof p4[0] === "string" ? p4[0] : null;
+    for (const p5 of obj.plugins) {
+      const name = typeof p5 === "string" ? p5 : Array.isArray(p5) && typeof p5[0] === "string" ? p5[0] : null;
       if (name) edges.push({ edgeType: "imports", metadata: { module: name, dialect: "babel" } });
     }
   }
@@ -40450,7 +40824,7 @@ var JsonLanguagePlugin = class {
         obj = JSON.parse(source);
       } catch {
         try {
-          obj = JSON.parse(stripJsonComments(source));
+          obj = JSON.parse(stripJsonComments2(source));
         } catch {
           return ok32({ language: "json", status: "ok", symbols: [] });
         }
@@ -45345,8 +45719,8 @@ var SpringPlugin = class {
       const re = new RegExp(`@${annotation}\\s*(?:\\(\\s*(?:value\\s*=\\s*)?["']([^"']*)["']\\s*\\))?`, "g");
       let m;
       while ((m = re.exec(source)) !== null) {
-        const path107 = m[1] ?? "";
-        const uri = normalizePath(classPrefix + "/" + path107);
+        const path108 = m[1] ?? "";
+        const uri = normalizePath(classPrefix + "/" + path108);
         result.routes.push({ method, uri, line: source.substring(0, m.index).split("\n").length });
       }
     }
@@ -45406,8 +45780,8 @@ var SpringPlugin = class {
     }
   }
 };
-function normalizePath(path107) {
-  return "/" + path107.replace(/\/+/g, "/").replace(/^\/|\/$/g, "");
+function normalizePath(path108) {
+  return "/" + path108.replace(/\/+/g, "/").replace(/^\/|\/$/g, "");
 }
 
 // src/indexer/plugins/integration/framework/express/index.ts
@@ -46915,8 +47289,8 @@ var NextJSPlugin = class {
       const fileSymbols = ctx.getSymbolsByFile(file.id);
       const fileSym = fileSymbols.find((s) => s.kind === "function" || s.kind === "class");
       if (!fileSym) continue;
-      const targetPage = pages.find((p4) => {
-        const pageRoute = appRouterPathToRoute(p4.path);
+      const targetPage = pages.find((p5) => {
+        const pageRoute = appRouterPathToRoute(p5.path);
         return pageRoute === info.interceptedRoute;
       });
       if (targetPage) {
@@ -48675,8 +49049,8 @@ var RawSqlPlugin = class {
         ...pkg.dependencies,
         ...pkg.devDependencies
       };
-      for (const p4 of RAW_SQL_PACKAGES) {
-        if (p4 in deps) return true;
+      for (const p5 of RAW_SQL_PACKAGES) {
+        if (p5 in deps) return true;
       }
     } catch {
     }
@@ -49363,8 +49737,8 @@ function extractExpoNavigationCalls(source) {
   }
   const templateRegex = /router\.(push|replace|navigate)\s*\(\s*`([^`]+)`/g;
   while ((match = templateRegex.exec(source)) !== null) {
-    const path107 = match[2].replace(/\$\{[^}]+\}/g, ":param");
-    paths.push(path107);
+    const path108 = match[2].replace(/\$\{[^}]+\}/g, ":param");
+    paths.push(path108);
   }
   const linkRegex = /<Link\s+[^>]*href\s*=\s*(?:\{?\s*)?['"]([^'"]+)['"]/g;
   while ((match = linkRegex.exec(source)) !== null) {
@@ -49376,9 +49750,9 @@ function extractExpoNavigationCalls(source) {
   }
   return [...new Set(paths)];
 }
-function matchExpoRoute(path107, routePattern) {
-  if (path107 === routePattern) return true;
-  const pathParts = path107.split("/").filter(Boolean);
+function matchExpoRoute(path108, routePattern) {
+  if (path108 === routePattern) return true;
+  const pathParts = path108.split("/").filter(Boolean);
   const routeParts = routePattern.split("/").filter(Boolean);
   if (pathParts.length !== routeParts.length) {
     if (routeParts[routeParts.length - 1] === "*" && pathParts.length >= routeParts.length - 1) {
@@ -50336,7 +50710,7 @@ var ShadcnPlugin = class {
       name: comp.name,
       kind: "component",
       framework: "shadcn-vue",
-      props: Object.fromEntries(comp.props.map((p4) => [p4, true])),
+      props: Object.fromEntries(comp.props.map((p5) => [p5, true])),
       emits: comp.emits,
       slots: comp.slots
     });
@@ -51323,7 +51697,7 @@ var NuxtUiPlugin = class {
             name: usage.name,
             kind: "component",
             framework: isPro ? "nuxt-ui-pro" : "nuxt-ui",
-            props: Object.fromEntries(usage.propsUsed.map((p4) => [p4, true]))
+            props: Object.fromEntries(usage.propsUsed.map((p5) => [p5, true]))
           });
           result.edges.push({
             edgeType: isPro ? "nuxt_ui_pro_component" : "nuxt_ui_component",
@@ -53466,11 +53840,11 @@ function detectTestFramework(source, _filePath) {
 function extractTestedRoutes(source) {
   const routes = [];
   const seen = /* @__PURE__ */ new Set();
-  function add(p4, method) {
-    const key = `${method ?? ""}:${p4}`;
+  function add(p5, method) {
+    const key = `${method ?? ""}:${p5}`;
     if (!seen.has(key)) {
       seen.add(key);
-      routes.push({ path: p4, method });
+      routes.push({ path: p5, method });
     }
   }
   let m;
@@ -55374,8 +55748,8 @@ var CommanderPlugin = class {
         ...pkg.dependencies,
         ...pkg.devDependencies
       };
-      for (const p4 of CLI_PACKAGES) {
-        if (p4 in deps) return true;
+      for (const p5 of CLI_PACKAGES) {
+        if (p5 in deps) return true;
       }
     } catch {
       return false;
@@ -55472,8 +55846,8 @@ var TreeSitterPlugin = class {
         ...pkg.dependencies,
         ...pkg.devDependencies
       };
-      for (const p4 of TREE_SITTER_PACKAGES) {
-        if (p4 in deps) return true;
+      for (const p5 of TREE_SITTER_PACKAGES) {
+        if (p5 in deps) return true;
       }
     } catch {
       return false;
@@ -55603,8 +55977,8 @@ var BuildToolsPlugin = class {
         ...pkg.dependencies,
         ...pkg.devDependencies
       };
-      for (const p4 of BUILD_PACKAGES) {
-        if (p4 in deps) return true;
+      for (const p5 of BUILD_PACKAGES) {
+        if (p5 in deps) return true;
       }
     } catch {
       return false;
@@ -55750,8 +56124,8 @@ var PinoPlugin = class {
         ...pkg.dependencies,
         ...pkg.devDependencies
       };
-      for (const p4 of LOGGING_PACKAGES) {
-        if (p4 in deps) return true;
+      for (const p5 of LOGGING_PACKAGES) {
+        if (p5 in deps) return true;
       }
     } catch {
       return false;
@@ -55825,8 +56199,8 @@ var CosmiconfigPlugin = class {
         ...pkg.dependencies,
         ...pkg.devDependencies
       };
-      for (const p4 of CONFIG_PACKAGES) {
-        if (p4 in deps) return true;
+      for (const p5 of CONFIG_PACKAGES) {
+        if (p5 in deps) return true;
       }
     } catch {
       return false;
@@ -55897,8 +56271,8 @@ var NeverthrowPlugin = class {
         ...pkg.dependencies,
         ...pkg.devDependencies
       };
-      for (const p4 of RESULT_PACKAGES) {
-        if (p4 in deps) return true;
+      for (const p5 of RESULT_PACKAGES) {
+        if (p5 in deps) return true;
       }
     } catch {
       return false;
@@ -55978,8 +56352,8 @@ var ClackPlugin = class {
         ...pkg.dependencies,
         ...pkg.devDependencies
       };
-      for (const p4 of PROMPT_PACKAGES) {
-        if (p4 in deps) return true;
+      for (const p5 of PROMPT_PACKAGES) {
+        if (p5 in deps) return true;
       }
     } catch {
       return false;
@@ -56109,9 +56483,9 @@ var FileWatcher2 = class {
           logger.error({ error: err32 }, "Watcher error");
           return;
         }
-        const notIgnored = (p4) => {
-          if (ignoreDirs.some((d) => p4.startsWith(d))) return false;
-          const rel = path92.relative(rootPath, p4);
+        const notIgnored = (p5) => {
+          if (ignoreDirs.some((d) => p5.startsWith(d))) return false;
+          const rel = path92.relative(rootPath, p5);
           return !traceignore.isIgnored(rel);
         };
         const changed = events.filter((e) => e.type === "create" || e.type === "update").map((e) => e.path).filter(notIgnored);
@@ -56121,7 +56495,7 @@ var FileWatcher2 = class {
           await onDeletes(deleted);
         }
         if (changed.length === 0) return;
-        for (const p4 of changed) this.pendingPaths.add(p4);
+        for (const p5 of changed) this.pendingPaths.add(p5);
         if (this.debounceTimer) this._clearTimeout(this.debounceTimer);
         this.debounceTimer = this._setTimeout(async () => {
           const paths = Array.from(this.pendingPaths);
@@ -56155,6 +56529,122 @@ var FileWatcher2 = class {
   }
 };
 
+// src/progress.ts
+function idleProgress() {
+  return { phase: "idle", processed: 0, total: 0, startedAt: 0, completedAt: 0 };
+}
+function snapOne(p5) {
+  const now = Date.now();
+  const endTime = p5.completedAt > 0 ? p5.completedAt : now;
+  return {
+    ...p5,
+    percentage: p5.total > 0 ? Math.round(p5.processed / p5.total * 100) : null,
+    elapsedMs: p5.startedAt > 0 ? endTime - p5.startedAt : 0
+  };
+}
+var ProgressState = class {
+  indexing = idleProgress();
+  summarization = idleProgress();
+  embedding = idleProgress();
+  db;
+  constructor(db) {
+    this.db = db ?? null;
+    if (this.db) {
+      this.loadFromDb();
+    }
+  }
+  update(name, partial) {
+    const current = this[name];
+    Object.assign(current, partial);
+    this.persist(name);
+    if (partial.phase === "running" && partial.total !== void 0) {
+      logger.info({ pipeline: name, total: current.total }, "%s started: %d items to process", name, current.total);
+    } else if (partial.phase === "completed") {
+      const elapsed = current.completedAt > 0 && current.startedAt > 0 ? Math.round((current.completedAt - current.startedAt) / 1e3) : 0;
+      logger.info({ pipeline: name, processed: current.processed, elapsed }, "%s completed: %d items in %ds", name, current.processed, elapsed);
+    } else if (partial.phase === "error") {
+      logger.error({ pipeline: name, error: current.error }, "%s failed: %s", name, current.error);
+    } else if (partial.processed !== void 0 && current.total > 0) {
+      const pct = Math.round(current.processed / current.total * 100);
+      logger.info({ pipeline: name, processed: current.processed, total: current.total, pct }, "%s progress: %d/%d (%d%%)", name, current.processed, current.total, pct);
+    }
+  }
+  snapshot() {
+    return {
+      indexing: snapOne(this.indexing),
+      summarization: snapOne(this.summarization),
+      embedding: snapOne(this.embedding)
+    };
+  }
+  persist(name) {
+    if (!this.db) return;
+    const p5 = this[name];
+    try {
+      this.db.prepare(`
+        INSERT OR REPLACE INTO indexing_progress
+          (pipeline, phase, processed, total, started_at, completed_at, error, updated_at)
+        VALUES (?, ?, ?, ?, ?, ?, ?, ?)
+      `).run(
+        name,
+        p5.phase,
+        p5.processed,
+        p5.total,
+        p5.startedAt,
+        p5.completedAt,
+        p5.error ?? null,
+        Date.now()
+      );
+    } catch (e) {
+      logger.debug({ error: e }, "Failed to persist progress");
+    }
+  }
+  loadFromDb() {
+    if (!this.db) return;
+    try {
+      const rows = this.db.prepare("SELECT * FROM indexing_progress").all();
+      for (const row of rows) {
+        if (row.pipeline in this) {
+          this[row.pipeline] = {
+            phase: row.phase,
+            processed: row.processed,
+            total: row.total,
+            startedAt: row.started_at,
+            completedAt: row.completed_at,
+            error: row.error ?? void 0
+          };
+        }
+      }
+    } catch {
+    }
+  }
+};
+function readProgressFromDb(db) {
+  try {
+    const rows = db.prepare("SELECT * FROM indexing_progress").all();
+    if (rows.length === 0) return null;
+    const map = new Map(rows.map((r) => [r.pipeline, r]));
+    const toProgress = (name) => {
+      const r = map.get(name);
+      if (!r) return idleProgress();
+      return {
+        phase: r.phase,
+        processed: r.processed,
+        total: r.total,
+        startedAt: r.started_at,
+        completedAt: r.completed_at,
+        error: r.error ?? void 0
+      };
+    };
+    return {
+      indexing: snapOne(toProgress("indexing")),
+      summarization: snapOne(toProgress("summarization")),
+      embedding: snapOne(toProgress("embedding"))
+    };
+  } catch {
+    return null;
+  }
+}
+
 // src/cli.ts
 import http from "http";
 
@@ -56430,7 +56920,7 @@ import path95 from "path";
 import os6 from "os";
 
 // src/init/types.ts
-var GUARD_HOOK_VERSION = "0.4.0";
+var GUARD_HOOK_VERSION = "0.5.0";
 var REINDEX_HOOK_VERSION = "0.1.0";
 var PRECOMPACT_HOOK_VERSION = "0.1.0";
 var WORKTREE_HOOK_VERSION = "0.1.0";
@@ -56452,7 +56942,7 @@ var CLIENTS = [
 var GUARD_HOOK = {
   scriptName: "trace-mcp-guard",
   settingsKey: "PreToolUse",
-  matcher: "Read|Grep|Glob|Bash",
+  matcher: "Read|Grep|Glob|Bash|Agent",
   version: GUARD_HOOK_VERSION,
   dryRunLabel: "Would install guard hook"
 };
@@ -56542,7 +57032,10 @@ function removeHookEntry(settings, desc) {
   const entries = hooks[desc.settingsKey];
   if (!Array.isArray(entries)) return;
   hooks[desc.settingsKey] = entries.filter(
-    (h) => !h.hooks?.some((hh) => hh.command?.includes(desc.scriptName))
+    (h) => {
+      const entry = h;
+      return !entry.hooks?.some((hh) => hh.command?.includes(desc.scriptName));
+    }
   );
   if (hooks[desc.settingsKey].length === 0) delete hooks[desc.settingsKey];
   if (Object.keys(hooks).length === 0) delete settings.hooks;
@@ -56720,12 +57213,12 @@ function detectProject(dir) {
   const ctx = buildProjectContext(projectRoot);
   const packageManagers = detectPackageManagers(projectRoot);
   const registry = new PluginRegistry();
-  for (const p4 of createAllLanguagePlugins()) registry.registerLanguagePlugin(p4);
-  for (const p4 of createAllIntegrationPlugins()) registry.registerFrameworkPlugin(p4);
+  for (const p5 of createAllLanguagePlugins()) registry.registerLanguagePlugin(p5);
+  for (const p5 of createAllIntegrationPlugins()) registry.registerFrameworkPlugin(p5);
   const activeResult = registry.getActiveFrameworkPlugins(ctx);
-  const frameworks = activeResult.isOk() ? activeResult.value.map((p4) => {
-    const dep = ctx.allDependencies.find((d) => d.name === p4.manifest.name);
-    return { name: p4.manifest.name, version: dep?.version, category: p4.manifest.category };
+  const frameworks = activeResult.isOk() ? activeResult.value.map((p5) => {
+    const dep = ctx.allDependencies.find((d) => d.name === p5.manifest.name);
+    return { name: p5.manifest.name, version: dep?.version, category: p5.manifest.category };
   }) : [];
   const languageMap = {
     node: "TypeScript",
@@ -56843,8 +57336,8 @@ function detectExistingConfig(root) {
     path97.join(root, ".trace-mcp.json"),
     path97.join(root, ".config", "trace-mcp.json")
   ];
-  for (const p4 of candidates) {
-    if (fs84.existsSync(p4)) return { path: p4 };
+  for (const p5 of candidates) {
+    if (fs84.existsSync(p5)) return { path: p5 };
   }
   const pkgPath = path97.join(root, "package.json");
   if (fs84.existsSync(pkgPath)) {
@@ -56858,7 +57351,7 @@ function detectExistingConfig(root) {
 }
 function detectExistingDb(root, globalDbPath) {
   const candidates = globalDbPath ? [globalDbPath, path97.join(root, ".trace-mcp", "index.db")] : [path97.join(root, ".trace-mcp", "index.db")];
-  const dbPath = candidates.find((p4) => fs84.existsSync(p4));
+  const dbPath = candidates.find((p5) => fs84.existsSync(p5));
   if (!dbPath) return null;
   try {
     const db = new Database6(dbPath, { readonly: true });
@@ -57469,9 +57962,9 @@ function scanGlobalArtifacts() {
   }
   return conflicts;
 }
-function shortPath(p4) {
-  if (p4.startsWith(HOME4)) return "~" + p4.slice(HOME4.length);
-  return p4;
+function shortPath(p5) {
+  if (p5.startsWith(HOME4)) return "~" + p5.slice(HOME4.length);
+  return p5;
 }
 function truncate(s, maxLen) {
   return s.length > maxLen ? s.slice(0, maxLen - 1) + "\u2026" : s;
@@ -57754,10 +58247,10 @@ function fixGlobalArtifact(conflict, opts) {
     return { conflictId: conflict.id, action: "skipped", detail: `Failed to remove: ${err32.message}`, target: dirPath };
   }
 }
-function shortPath2(p4) {
+function shortPath2(p5) {
   const home = process.env.HOME ?? process.env.USERPROFILE ?? "";
-  if (home && p4.startsWith(home)) return "~" + p4.slice(home.length);
-  return p4;
+  if (home && p5.startsWith(home)) return "~" + p5.slice(home.length);
+  return p5;
 }
 
 // src/project-root.ts
@@ -58024,16 +58517,16 @@ function generateConfig(detection) {
   for (const fw of detection.frameworks) {
     const preset = FRAMEWORK_PRESETS[fw.name];
     if (preset) {
-      for (const p4 of preset.include) include.add(p4);
-      for (const p4 of preset.exclude) exclude.add(p4);
+      for (const p5 of preset.include) include.add(p5);
+      for (const p5 of preset.exclude) exclude.add(p5);
     }
   }
   if (include.size === 0) {
     for (const lang of detection.languages) {
       const preset = LANGUAGE_PRESETS[lang.toLowerCase()];
       if (preset) {
-        for (const p4 of preset.include) include.add(p4);
-        for (const p4 of preset.exclude) exclude.add(p4);
+        for (const p5 of preset.include) include.add(p5);
+        for (const p5 of preset.exclude) exclude.add(p5);
       }
     }
   }
@@ -58283,7 +58776,16 @@ var initCommand = new Command("init").description("One-time global setup: config
     }
   }
   if (indexProject) {
-    const indexStep = registerAndIndexProject(process.cwd(), { dryRun: opts.dryRun, force: opts.force });
+    const spin = !nonInteractive ? p.spinner() : null;
+    spin?.start("Registering and indexing current project...");
+    const indexStep = await registerAndIndexProject(process.cwd(), { dryRun: opts.dryRun, force: opts.force });
+    if (spin) {
+      if (indexStep.detail?.includes("Indexed")) {
+        spin.stop(indexStep.detail);
+      } else {
+        spin.stop(indexStep.detail ?? indexStep.action);
+      }
+    }
     steps.push(indexStep);
   }
   const existingProjects = listProjects();
@@ -58365,7 +58867,7 @@ var initCommand = new Command("init").description("One-time global setup: config
       p.note(lines.join("\n"), "Already configured");
     }
     p.outro(
-      indexProject ? "Ready! Project registered and will be indexed when trace-mcp serve starts." : "Ready! Run `trace-mcp add` in a project directory to register it for indexing."
+      indexProject ? "Ready! Project registered and indexed." : "Ready! Run `trace-mcp add` in a project directory to register it for indexing."
     );
   }
 });
@@ -58397,7 +58899,31 @@ function executeSteps(steps, opts) {
     steps.push(mdResult);
   }
 }
-function registerAndIndexProject(dir, opts) {
+function formatDuration(ms) {
+  if (ms < 1e3) return `${ms}ms`;
+  return `${(ms / 1e3).toFixed(1)}s`;
+}
+async function runIndexingForProject(projectRoot) {
+  const configResult = await loadConfig(projectRoot);
+  if (configResult.isErr()) return null;
+  const dbPath = getDbPath(projectRoot);
+  const db = initializeDatabase(dbPath);
+  const store = new Store(db);
+  const registry = new PluginRegistry();
+  for (const lp of createAllLanguagePlugins()) registry.registerLanguagePlugin(lp);
+  for (const fp of createAllIntegrationPlugins()) registry.registerFrameworkPlugin(fp);
+  const pipeline = new IndexingPipeline(store, registry, configResult.value, projectRoot);
+  try {
+    const result = await pipeline.indexAll(true);
+    updateLastIndexed(projectRoot);
+    return { indexed: result.indexed, skipped: result.skipped, errors: result.errors, durationMs: result.durationMs };
+  } catch {
+    return null;
+  } finally {
+    db.close();
+  }
+}
+async function registerAndIndexProject(dir, opts) {
   let projectRoot = null;
   try {
     projectRoot = findProjectRoot(dir);
@@ -58408,7 +58934,7 @@ function registerAndIndexProject(dir, opts) {
     if (childRoots.length === 0) {
       return { target: dir, action: "skipped", detail: "Could not detect project root or child projects" };
     }
-    return registerMultiRootProject(dir, childRoots, opts);
+    return await registerMultiRootProject(dir, childRoots, opts);
   }
   if (opts.dryRun) {
     return { target: projectRoot, action: "skipped", detail: "Would register and index project" };
@@ -58428,13 +58954,15 @@ function registerAndIndexProject(dir, opts) {
   const db = initializeDatabase(dbPath);
   db.close();
   const entry = registerProject(projectRoot);
+  const indexResult = await runIndexingForProject(projectRoot);
+  const detail = indexResult ? `Registered and indexed: ${entry.name} \u2014 ${indexResult.indexed} files in ${formatDuration(indexResult.durationMs)} (${indexResult.skipped} skipped, ${indexResult.errors} errors)` : `Registered project: ${entry.name} (indexing failed)`;
   return {
     target: projectRoot,
     action: existing ? "updated" : "created",
-    detail: `Registered project: ${entry.name}`
+    detail
   };
 }
-function registerMultiRootProject(parentDir, childRoots, opts) {
+async function registerMultiRootProject(parentDir, childRoots, opts) {
   if (opts.dryRun) {
     return {
       target: parentDir,
@@ -58474,10 +59002,12 @@ function registerMultiRootProject(parentDir, childRoots, opts) {
   const db = initializeDatabase(dbPath);
   db.close();
   const entry = registerProject(parentDir, { type: "multi-root", children: childRoots });
+  const indexResult = await runIndexingForProject(parentDir);
+  const detail = indexResult ? `Registered and indexed multi-root: ${entry.name} (${childRoots.length} children) \u2014 ${indexResult.indexed} files in ${formatDuration(indexResult.durationMs)}` : `Registered multi-root (${childRoots.length} children): ${childRoots.map((r) => path102.basename(r)).join(", ")} (indexing failed)`;
   return {
     target: parentDir,
     action: existing ? "updated" : "created",
-    detail: `Registered multi-root (${childRoots.length} children): ${childRoots.map((r) => path102.basename(r)).join(", ")}`
+    detail
   };
 }
 function formatClientName(name) {
@@ -58491,12 +59021,12 @@ function formatClientName(name) {
   };
   return names[name] ?? name;
 }
-function shortPath3(p4) {
+function shortPath3(p5) {
   const home = process.env.HOME ?? process.env.USERPROFILE ?? "";
-  if (home && p4.startsWith(home)) return "~" + p4.slice(home.length);
+  if (home && p5.startsWith(home)) return "~" + p5.slice(home.length);
   const cwd = process.cwd();
-  if (p4.startsWith(cwd)) return p4.slice(cwd.length + 1) || ".";
-  return p4;
+  if (p5.startsWith(cwd)) return p5.slice(cwd.length + 1) || ".";
+  return p5;
 }
 
 // src/cli/upgrade.ts
@@ -58513,11 +59043,11 @@ var upgradeCommand = new Command2("upgrade").description("Upgrade trace-mcp: run
       console.error("No registered projects. Run `trace-mcp add` first, or specify a directory.");
       process.exit(1);
     }
-    for (const p4 of projects) {
-      if (fs90.existsSync(p4.root)) {
-        projectRoots.push(p4.root);
+    for (const p5 of projects) {
+      if (fs90.existsSync(p5.root)) {
+        projectRoots.push(p5.root);
       } else {
-        logger.warn({ root: p4.root }, "Skipping stale project (directory not found)");
+        logger.warn({ root: p5.root }, "Skipping stale project (directory not found)");
       }
     }
   }
@@ -58547,8 +59077,8 @@ var upgradeCommand = new Command2("upgrade").description("Upgrade trace-mcp: run
         });
         if (!opts.skipReindex) {
           const registry = new PluginRegistry();
-          for (const p4 of createAllLanguagePlugins()) registry.registerLanguagePlugin(p4);
-          for (const p4 of createAllIntegrationPlugins()) registry.registerFrameworkPlugin(p4);
+          for (const p5 of createAllLanguagePlugins()) registry.registerLanguagePlugin(p5);
+          for (const p5 of createAllIntegrationPlugins()) registry.registerFrameworkPlugin(p5);
           const pipeline = new IndexingPipeline(store, registry, config, projectRoot);
           const result = await pipeline.indexAll(true);
           steps.push({
@@ -58611,7 +59141,39 @@ import { Command as Command3 } from "commander";
 import fs91 from "fs";
 import path104 from "path";
 import * as p2 from "@clack/prompts";
-var addCommand = new Command3("add").description("Register a project for indexing: detect root, create DB, add to registry").argument("[dir]", "Project directory (default: current directory)", ".").option("--force", "Re-register even if already registered").option("--json", "Output results as JSON").action(async (dir, opts) => {
+async function runIndexing(projectRoot, opts) {
+  const configResult = await loadConfig(projectRoot);
+  if (configResult.isErr()) {
+    if (!opts.json) {
+      p2.log.warn(`Could not load config for indexing: ${configResult.error}`);
+    }
+    return null;
+  }
+  const dbPath = getDbPath(projectRoot);
+  const db = initializeDatabase(dbPath);
+  const store = new Store(db);
+  const registry = new PluginRegistry();
+  for (const lp of createAllLanguagePlugins()) registry.registerLanguagePlugin(lp);
+  for (const fp of createAllIntegrationPlugins()) registry.registerFrameworkPlugin(fp);
+  const pipeline = new IndexingPipeline(store, registry, configResult.value, projectRoot);
+  try {
+    const result = await pipeline.indexAll(true);
+    updateLastIndexed(projectRoot);
+    return { indexed: result.indexed, skipped: result.skipped, errors: result.errors, durationMs: result.durationMs };
+  } catch (err32) {
+    if (!opts.json) {
+      p2.log.warn(`Indexing failed: ${err32.message}`);
+    }
+    return null;
+  } finally {
+    db.close();
+  }
+}
+function formatDuration2(ms) {
+  if (ms < 1e3) return `${ms}ms`;
+  return `${(ms / 1e3).toFixed(1)}s`;
+}
+var addCommand = new Command3("add").description("Register a project for indexing: detect root, create DB, add to registry").argument("[dir]", "Project directory (default: current directory)", ".").option("--force", "Re-register even if already registered").option("--no-index", "Skip indexing after registration").option("--json", "Output results as JSON").action(async (dir, opts) => {
   const resolvedDir = path104.resolve(dir);
   if (!fs91.existsSync(resolvedDir)) {
     console.error(`Directory does not exist: ${resolvedDir}`);
@@ -58697,6 +59259,21 @@ DB: ${shortPath4(existing.dbPath)}`, "Existing");
   const db = initializeDatabase(dbPath);
   db.close();
   const entry = registerProject(projectRoot);
+  let indexResult = null;
+  if (opts.index !== false) {
+    if (isInteractive) {
+      const spin = p2.spinner();
+      spin.start("Indexing project...");
+      indexResult = await runIndexing(projectRoot, opts);
+      if (indexResult) {
+        spin.stop(`Indexed ${indexResult.indexed} files in ${formatDuration2(indexResult.durationMs)}`);
+      } else {
+        spin.stop("Indexing skipped");
+      }
+    } else {
+      indexResult = await runIndexing(projectRoot, opts);
+    }
+  }
   if (opts.json) {
     console.log(JSON.stringify({
       status: existing ? "re-registered" : "registered",
@@ -58705,7 +59282,8 @@ DB: ${shortPath4(existing.dbPath)}`, "Existing");
       detection: {
         languages: detection.languages,
         frameworks: detection.frameworks.map((f) => f.name)
-      }
+      },
+      indexing: indexResult ?? void 0
     }, null, 2));
   } else {
     const lines = [];
@@ -58715,8 +59293,16 @@ DB: ${shortPath4(existing.dbPath)}`, "Existing");
     if (migrated) {
       lines.push(`Migrated existing index from .trace-mcp/index.db`);
     }
+    if (indexResult) {
+      lines.push(`Indexed: ${indexResult.indexed} files (${indexResult.skipped} skipped, ${indexResult.errors} errors)`);
+      lines.push(`Duration: ${formatDuration2(indexResult.durationMs)}`);
+    }
     p2.note(lines.join("\n"), existing ? "Re-registered" : "Registered");
-    p2.outro("Project registered. It will be indexed when trace-mcp serve starts.");
+    if (indexResult) {
+      p2.outro("Project registered and indexed.");
+    } else {
+      p2.outro("Project registered. Run `trace-mcp index` to index it.");
+    }
   }
 });
 async function handleMultiRoot(parentDir, childRoots, opts) {
@@ -58799,13 +59385,29 @@ Discovered ${childRoots.length} child project(s):
     type: "multi-root",
     children: childRoots
   });
+  let indexResult = null;
+  if (opts.index !== false) {
+    if (isInteractive) {
+      const spin = p2.spinner();
+      spin.start("Indexing multi-root project...");
+      indexResult = await runIndexing(parentDir, opts);
+      if (indexResult) {
+        spin.stop(`Indexed ${indexResult.indexed} files in ${formatDuration2(indexResult.durationMs)}`);
+      } else {
+        spin.stop("Indexing skipped");
+      }
+    } else {
+      indexResult = await runIndexing(parentDir, opts);
+    }
+  }
   if (opts.json) {
     console.log(JSON.stringify({
       status: existing ? "re-registered" : "registered",
       type: "multi-root",
       project: entry,
       children: childRoots.map((r) => path104.basename(r)),
-      cleaned
+      cleaned,
+      indexing: indexResult ?? void 0
     }, null, 2));
   } else {
     const lines = [];
@@ -58813,14 +59415,22 @@ Discovered ${childRoots.length} child project(s):
     lines.push(`Root: ${parentDir}`);
     lines.push(`DB: ${shortPath4(dbPath)}`);
     lines.push(`Children: ${childRoots.map((r) => path104.basename(r)).join(", ")}`);
+    if (indexResult) {
+      lines.push(`Indexed: ${indexResult.indexed} files (${indexResult.skipped} skipped, ${indexResult.errors} errors)`);
+      lines.push(`Duration: ${formatDuration2(indexResult.durationMs)}`);
+    }
     p2.note(lines.join("\n"), existing ? "Re-registered" : "Registered");
-    p2.outro("Multi-root project registered. It will be indexed when trace-mcp serve starts.");
+    if (indexResult) {
+      p2.outro("Multi-root project registered and indexed.");
+    } else {
+      p2.outro("Multi-root project registered. Run `trace-mcp index` to index it.");
+    }
   }
 }
-function shortPath4(p4) {
+function shortPath4(p5) {
   const home = process.env.HOME ?? process.env.USERPROFILE ?? "";
-  if (home && p4.startsWith(home)) return "~" + p4.slice(home.length);
-  return p4;
+  if (home && p5.startsWith(home)) return "~" + p5.slice(home.length);
+  return p5;
 }
 
 // src/cli/doctor.ts
@@ -58882,11 +59492,11 @@ var doctorCommand = new Command4("doctor").description("Check for competing tool
       return;
     }
     if (!opts.dryRun) {
-      const confirm3 = await p3.confirm({
+      const confirm4 = await p3.confirm({
         message: `Fix ${fixable2.length} conflict${fixable2.length > 1 ? "s" : ""} automatically?`,
         initialValue: true
       });
-      if (p3.isCancel(confirm3) || !confirm3) {
+      if (p3.isCancel(confirm4) || !confirm4) {
         p3.cancel("No changes made.");
         return;
       }
@@ -58952,12 +59562,12 @@ function printFixResults(results, dryRun) {
     p3.outro("Dry run complete \u2014 no changes made. Run with --fix to apply.");
   }
 }
-function shortPath5(p4) {
+function shortPath5(p5) {
   const home = process.env.HOME ?? process.env.USERPROFILE ?? "";
-  if (home && p4.startsWith(home)) return "~" + p4.slice(home.length);
+  if (home && p5.startsWith(home)) return "~" + p5.slice(home.length);
   const cwd = process.cwd();
-  if (p4.startsWith(cwd)) return p4.slice(cwd.length + 1) || ".";
-  return p4;
+  if (p5.startsWith(cwd)) return p5.slice(cwd.length + 1) || ".";
+  return p5;
 }
 
 // src/cli/ci.ts
@@ -59321,8 +59931,8 @@ ${msg}
   const store = new Store(db);
   if (opts.index) {
     const registry = new PluginRegistry();
-    for (const p4 of createAllLanguagePlugins()) registry.registerLanguagePlugin(p4);
-    for (const p4 of createAllIntegrationPlugins()) registry.registerFrameworkPlugin(p4);
+    for (const p5 of createAllLanguagePlugins()) registry.registerLanguagePlugin(p5);
+    for (const p5 of createAllIntegrationPlugins()) registry.registerFrameworkPlugin(p5);
     logger.info("CI report: indexing project...");
     const pipeline = new IndexingPipeline(store, registry, config, projectRoot);
     await pipeline.indexAll(false);
@@ -59445,8 +60055,8 @@ var checkCommand = new Command6("check").description("Run quality gate checks ag
   const store = new Store(db);
   if (opts.index) {
     const registry = new PluginRegistry();
-    for (const p4 of createAllLanguagePlugins()) registry.registerLanguagePlugin(p4);
-    for (const p4 of createAllIntegrationPlugins()) registry.registerFrameworkPlugin(p4);
+    for (const p5 of createAllLanguagePlugins()) registry.registerLanguagePlugin(p5);
+    for (const p5 of createAllIntegrationPlugins()) registry.registerFrameworkPlugin(p5);
     logger.info("Indexing project before quality check...");
     const pipeline = new IndexingPipeline(store, registry, config, projectRoot);
     await pipeline.indexAll(false);
@@ -59928,13 +60538,269 @@ analyticsCommand.command("trends").description("Show daily usage trends: tokens,
   }
 });
 
+// src/cli/remove.ts
+import { Command as Command10 } from "commander";
+import fs94 from "fs";
+import path106 from "path";
+import * as p4 from "@clack/prompts";
+var removeCommand = new Command10("remove").description("Unregister a project and delete its index").argument("[dir]", "Project directory (default: current directory)", ".").option("--force", "Remove without confirmation").option("--keep-db", "Keep the database file (only unregister)").option("--json", "Output results as JSON").action(async (dir, opts) => {
+  const resolvedDir = path106.resolve(dir);
+  const isInteractive = !opts.json;
+  let projectRoot;
+  try {
+    projectRoot = findProjectRoot(resolvedDir);
+  } catch {
+    projectRoot = resolvedDir;
+  }
+  const parentEntry = findParentProject(projectRoot);
+  if (parentEntry) {
+    await handleRemoveFromMultiRoot(projectRoot, parentEntry, opts);
+    return;
+  }
+  const entry = getProject(projectRoot);
+  if (!entry) {
+    if (opts.json) {
+      console.log(JSON.stringify({ status: "not_registered", dir: projectRoot }));
+    } else {
+      if (isInteractive) p4.intro("trace-mcp remove");
+      p4.log.warn(`Project not registered: ${projectRoot}`);
+      p4.log.info("Use `trace-mcp list` to see registered projects.");
+    }
+    return;
+  }
+  if (isInteractive) {
+    p4.intro("trace-mcp remove");
+    const lines = [];
+    lines.push(`Project: ${entry.name}`);
+    lines.push(`Root: ${entry.root}`);
+    lines.push(`DB: ${shortPath6(entry.dbPath)}`);
+    if (entry.type === "multi-root" && entry.children) {
+      lines.push(`Children: ${entry.children.map((c) => path106.basename(c)).join(", ")}`);
+    }
+    p4.note(lines.join("\n"), "Project to remove");
+  }
+  if (!opts.force && isInteractive) {
+    const confirm4 = await p4.confirm({
+      message: entry.type === "multi-root" ? `Remove multi-root project "${entry.name}" and its unified index?` : `Remove project "${entry.name}" and delete its index?`,
+      initialValue: false
+    });
+    if (p4.isCancel(confirm4) || !confirm4) {
+      p4.cancel("Cancelled.");
+      return;
+    }
+  }
+  let dbDeleted = false;
+  if (!opts.keepDb && fs94.existsSync(entry.dbPath)) {
+    fs94.unlinkSync(entry.dbPath);
+    dbDeleted = true;
+  }
+  removeProjectConfig(entry.root);
+  unregisterProject(entry.root);
+  if (opts.json) {
+    console.log(JSON.stringify({
+      status: "removed",
+      project: entry.name,
+      root: entry.root,
+      dbDeleted
+    }, null, 2));
+  } else {
+    const lines = [];
+    lines.push(`Project: ${entry.name}`);
+    if (dbDeleted) {
+      lines.push(`Database deleted: ${shortPath6(entry.dbPath)}`);
+    } else if (opts.keepDb) {
+      lines.push(`Database kept: ${shortPath6(entry.dbPath)}`);
+    }
+    lines.push("Config removed");
+    p4.note(lines.join("\n"), "Removed");
+    p4.outro("Project unregistered.");
+  }
+});
+async function handleRemoveFromMultiRoot(childRoot, parent, opts) {
+  const isInteractive = !opts.json;
+  if (isInteractive) {
+    p4.intro("trace-mcp remove (from multi-root)");
+    p4.note(
+      `This project is part of multi-root index: ${parent.name}
+Parent root: ${parent.root}
+Child to exclude: ${path106.basename(childRoot)}`,
+      "Multi-root"
+    );
+  }
+  if (!opts.force && isInteractive) {
+    const confirm4 = await p4.confirm({
+      message: `Exclude "${path106.basename(childRoot)}" from multi-root "${parent.name}"? (The parent index will be re-registered without this child.)`,
+      initialValue: false
+    });
+    if (p4.isCancel(confirm4) || !confirm4) {
+      p4.cancel("Cancelled.");
+      return;
+    }
+  }
+  const currentChildren = parent.children ?? [];
+  const newChildren = currentChildren.filter((c) => path106.resolve(c) !== path106.resolve(childRoot));
+  if (newChildren.length === 0) {
+    if (!opts.keepDb && fs94.existsSync(parent.dbPath)) {
+      fs94.unlinkSync(parent.dbPath);
+    }
+    removeProjectConfig(parent.root);
+    unregisterProject(parent.root);
+    if (opts.json) {
+      console.log(JSON.stringify({
+        status: "removed_multi_root",
+        reason: "no children remaining",
+        parent: parent.name
+      }, null, 2));
+    } else {
+      p4.note("No children remaining \u2014 entire multi-root project removed.", "Removed");
+      p4.outro("Multi-root project unregistered.");
+    }
+    return;
+  }
+  if (newChildren.length === 1) {
+    const remainingChild = newChildren[0];
+    if (!opts.keepDb && fs94.existsSync(parent.dbPath)) {
+      fs94.unlinkSync(parent.dbPath);
+    }
+    removeProjectConfig(parent.root);
+    unregisterProject(parent.root);
+    if (opts.json) {
+      console.log(JSON.stringify({
+        status: "excluded_from_multi_root",
+        excluded: path106.basename(childRoot),
+        remaining: path106.basename(remainingChild),
+        hint: `Run \`trace-mcp add ${remainingChild}\` to re-register the remaining project individually.`
+      }, null, 2));
+    } else {
+      p4.note(
+        `Excluded: ${path106.basename(childRoot)}
+Only one child remaining: ${path106.basename(remainingChild)}
+Multi-root removed. Run \`trace-mcp add ${remainingChild}\` to re-register individually.`,
+        "Converted"
+      );
+      p4.outro("Child excluded from multi-root.");
+    }
+    return;
+  }
+  if (!opts.keepDb && fs94.existsSync(parent.dbPath)) {
+    fs94.unlinkSync(parent.dbPath);
+  }
+  removeProjectConfig(parent.root);
+  unregisterProject(parent.root);
+  if (opts.json) {
+    console.log(JSON.stringify({
+      status: "excluded_from_multi_root",
+      excluded: path106.basename(childRoot),
+      remaining: newChildren.map((c) => path106.basename(c)),
+      hint: `Run \`trace-mcp add ${parent.root}\` to re-register with ${newChildren.length} children.`
+    }, null, 2));
+  } else {
+    p4.note(
+      `Excluded: ${path106.basename(childRoot)}
+Remaining children: ${newChildren.map((c) => path106.basename(c)).join(", ")}
+Run \`trace-mcp add ${parent.root}\` to re-register the multi-root.`,
+      "Excluded"
+    );
+    p4.outro("Child excluded. Re-add the parent to rebuild the index.");
+  }
+}
+function shortPath6(p5) {
+  const home = process.env.HOME ?? process.env.USERPROFILE ?? "";
+  if (home && p5.startsWith(home)) return "~" + p5.slice(home.length);
+  return p5;
+}
+
+// src/cli/status.ts
+import { Command as Command11 } from "commander";
+import fs95 from "fs";
+import Database7 from "better-sqlite3";
+function resolveDbPath5(projectRoot) {
+  const entry = getProject(projectRoot);
+  if (entry) return entry.dbPath;
+  return getDbPath(projectRoot);
+}
+function formatDuration3(ms) {
+  if (ms < 1e3) return `${ms}ms`;
+  const s = Math.round(ms / 1e3);
+  if (s < 60) return `${s}s`;
+  const m = Math.floor(s / 60);
+  const rem = s % 60;
+  return rem > 0 ? `${m}m ${rem}s` : `${m}m`;
+}
+function formatPipeline(name, p5) {
+  const label = name.padEnd(16);
+  switch (p5.phase) {
+    case "idle":
+      return `  ${label} idle`;
+    case "running": {
+      const pct = p5.percentage !== null ? `(${p5.percentage}%)` : "";
+      const count = p5.total > 0 ? `${p5.processed}/${p5.total}` : `${p5.processed}`;
+      const elapsed = p5.elapsedMs > 0 ? `  ${formatDuration3(p5.elapsedMs)} elapsed` : "";
+      return `  ${label} running    ${count} ${pct}${elapsed}`;
+    }
+    case "completed": {
+      const count = p5.total > 0 ? `${p5.processed}/${p5.total}` : `${p5.processed}`;
+      const elapsed = p5.elapsedMs > 0 ? `  ${formatDuration3(p5.elapsedMs)}` : "";
+      return `  ${label} completed  ${count} (100%)${elapsed}`;
+    }
+    case "error":
+      return `  ${label} error      ${p5.error ?? "unknown error"}`;
+    default:
+      return `  ${label} ${p5.phase}`;
+  }
+}
+var statusCommand = new Command11("status").description("Show indexing progress for the current project").option("--json", "Output as JSON").action((opts) => {
+  let projectRoot;
+  try {
+    projectRoot = findProjectRoot(process.cwd());
+  } catch {
+    projectRoot = process.cwd();
+  }
+  const dbPath = resolveDbPath5(projectRoot);
+  if (!fs95.existsSync(dbPath)) {
+    console.log(`No index found for ${projectRoot}`);
+    console.log("Run `trace-mcp serve` or `trace-mcp index` first.");
+    process.exit(1);
+  }
+  const db = new Database7(dbPath, { readonly: true });
+  db.pragma("journal_mode = WAL");
+  try {
+    const progress = readProgressFromDb(db);
+    const stats = db.prepare(`
+        SELECT
+          (SELECT COUNT(*) FROM files) as files,
+          (SELECT COUNT(*) FROM symbols) as symbols,
+          (SELECT COUNT(*) FROM edges) as edges
+      `).get();
+    if (opts.json) {
+      console.log(JSON.stringify({ projectRoot, stats, progress }, null, 2));
+      return;
+    }
+    console.log(`
+trace-mcp status \u2014 ${projectRoot}
+`);
+    if (progress) {
+      console.log(formatPipeline("Indexing:", progress.indexing));
+      console.log(formatPipeline("Summarization:", progress.summarization));
+      console.log(formatPipeline("Embedding:", progress.embedding));
+    } else {
+      console.log("  No progress data available (server may not have run yet)");
+    }
+    console.log(`
+  Stats: ${stats.files} files \xB7 ${stats.symbols} symbols \xB7 ${stats.edges} edges
+`);
+  } finally {
+    db.close();
+  }
+});
+
 // src/cli.ts
-var PKG_VERSION2 = true ? "1.6.1" : "0.0.0-dev";
+var PKG_VERSION2 = true ? "1.7.0" : "0.0.0-dev";
 function registerDefaultPlugins(registry) {
-  for (const p4 of createAllLanguagePlugins()) registry.registerLanguagePlugin(p4);
-  for (const p4 of createAllIntegrationPlugins()) registry.registerFrameworkPlugin(p4);
+  for (const p5 of createAllLanguagePlugins()) registry.registerLanguagePlugin(p5);
+  for (const p5 of createAllIntegrationPlugins()) registry.registerFrameworkPlugin(p5);
 }
-function resolveDbPath5(projectRoot) {
+function resolveDbPath6(projectRoot) {
   const entry = getProject(projectRoot);
   if (entry) return entry.dbPath;
   return getDbPath(projectRoot);
@@ -59968,7 +60834,7 @@ function runFederationAutoSync(projectRoot, config) {
     logger.warn({ error: e }, "Federation auto-sync failed (non-fatal)");
   }
 }
-var program = new Command10();
+var program = new Command12();
 program.name("trace-mcp").description("Framework-Aware Code Intelligence for Laravel/Vue/Inertia/Nuxt").version(PKG_VERSION2);
 program.command("serve").description("Start MCP server (stdio transport)").action(async () => {
   const projectRoot = process.cwd();
@@ -59988,18 +60854,19 @@ program.command("serve").description("Start MCP server (stdio transport)").actio
     process.exit(1);
   }
   const config = configResult.value;
-  const dbPath = resolveDbPath5(projectRoot);
+  const dbPath = resolveDbPath6(projectRoot);
   ensureGlobalDirs();
   const db = initializeDatabase(dbPath);
   const store = new Store(db);
   const registry = new PluginRegistry();
   registerDefaultPlugins(registry);
-  const pipeline = new IndexingPipeline(store, registry, config, projectRoot);
+  const progress = new ProgressState(db);
+  const pipeline = new IndexingPipeline(store, registry, config, projectRoot, progress);
   const watcher = new FileWatcher2();
   const aiProvider = createAIProvider(config);
   const vectorStore = config.ai?.enabled ? new BlobVectorStore(store.db) : null;
   const embeddingService = config.ai?.enabled ? aiProvider.embedding() : null;
-  const embeddingPipeline = vectorStore && embeddingService ? new EmbeddingPipeline(store, embeddingService, vectorStore) : null;
+  const embeddingPipeline = vectorStore && embeddingService ? new EmbeddingPipeline(store, embeddingService, vectorStore, progress) : null;
   const inferenceCache = config.ai?.enabled ? new InferenceCache(store.db) : null;
   inferenceCache?.evictExpired();
   const summarizationPipeline = config.ai?.enabled && config.ai.summarize_on_index !== false ? new SummarizationPipeline(
@@ -60010,7 +60877,8 @@ program.command("serve").description("Start MCP server (stdio transport)").actio
       batchSize: config.ai.summarize_batch_size ?? 20,
       kinds: config.ai.summarize_kinds ?? ["class", "function", "method", "interface", "trait", "enum", "type"],
       concurrency: config.ai.concurrency ?? 1
-    }
+    },
+    progress
   ) : null;
   const runEmbeddings = () => {
     if (!embeddingPipeline) return;
@@ -60044,7 +60912,7 @@ program.command("serve").description("Start MCP server (stdio transport)").actio
   };
   process.on("SIGINT", shutdown);
   process.on("SIGTERM", shutdown);
-  const server = createServer2(store, registry, config, projectRoot);
+  const server = createServer2(store, registry, config, projectRoot, progress);
   const transport = new StdioServerTransport();
   logger.info({ projectRoot, dbPath }, "Starting trace-mcp MCP server...");
   await server.connect(transport);
@@ -60057,18 +60925,19 @@ program.command("serve-http").description("Start MCP server (HTTP/SSE transport)
     process.exit(1);
   }
   const config = configResult.value;
-  const dbPath = resolveDbPath5(projectRoot);
+  const dbPath = resolveDbPath6(projectRoot);
   ensureGlobalDirs();
   const db = initializeDatabase(dbPath);
   const store = new Store(db);
   const registry = new PluginRegistry();
   registerDefaultPlugins(registry);
-  const pipeline = new IndexingPipeline(store, registry, config, projectRoot);
+  const progress2 = new ProgressState(db);
+  const pipeline = new IndexingPipeline(store, registry, config, projectRoot, progress2);
   const watcher = new FileWatcher2();
   const aiProvider = createAIProvider(config);
   const vectorStore = config.ai?.enabled ? new BlobVectorStore(store.db) : null;
   const embeddingService = config.ai?.enabled ? aiProvider.embedding() : null;
-  const embeddingPipeline = vectorStore && embeddingService ? new EmbeddingPipeline(store, embeddingService, vectorStore) : null;
+  const embeddingPipeline = vectorStore && embeddingService ? new EmbeddingPipeline(store, embeddingService, vectorStore, progress2) : null;
   const inferenceCache2 = config.ai?.enabled ? new InferenceCache(store.db) : null;
   inferenceCache2?.evictExpired();
   const summarizationPipeline2 = config.ai?.enabled && config.ai.summarize_on_index !== false ? new SummarizationPipeline(
@@ -60079,7 +60948,8 @@ program.command("serve-http").description("Start MCP server (HTTP/SSE transport)
       batchSize: config.ai.summarize_batch_size ?? 20,
       kinds: config.ai.summarize_kinds ?? ["class", "function", "method", "interface", "trait", "enum", "type"],
       concurrency: config.ai.concurrency ?? 1
-    }
+    },
+    progress2
   ) : null;
   const runEmbeddings = () => {
     if (!embeddingPipeline) return;
@@ -60109,7 +60979,7 @@ program.command("serve-http").description("Start MCP server (HTTP/SSE transport)
   });
   const port = parseInt(opts.port, 10);
   const host = opts.host;
-  const server = createServer2(store, registry, config, projectRoot);
+  const server = createServer2(store, registry, config, projectRoot, progress2);
   const transport = new StreamableHTTPServerTransport({
     sessionIdGenerator: () => randomUUID()
   });
@@ -60211,8 +61081,8 @@ program.command("serve-http").description("Start MCP server (HTTP/SSE transport)
   });
 });
 program.command("index").description("Index a project directory").argument("<dir>", "Directory to index").option("-f, --force", "Force reindex all files").action(async (dir, opts) => {
-  const resolvedDir = path106.resolve(dir);
-  if (!fs94.existsSync(resolvedDir)) {
+  const resolvedDir = path107.resolve(dir);
+  if (!fs96.existsSync(resolvedDir)) {
     logger.error({ dir: resolvedDir }, "Directory does not exist");
     process.exit(1);
   }
@@ -60222,7 +61092,7 @@ program.command("index").description("Index a project directory").argument("<dir
     process.exit(1);
   }
   const config = configResult.value;
-  const dbPath = resolveDbPath5(resolvedDir);
+  const dbPath = resolveDbPath6(resolvedDir);
   ensureGlobalDirs();
   const db = initializeDatabase(dbPath);
   const store = new Store(db);
@@ -60236,20 +61106,20 @@ program.command("index").description("Index a project directory").argument("<dir
   db.close();
 });
 program.command("index-file").description("Incrementally reindex a single file (called by the PostToolUse auto-reindex hook)").argument("<file>", "Absolute or relative path to the file to reindex").action(async (file) => {
-  const resolvedFile = path106.resolve(file);
-  if (!fs94.existsSync(resolvedFile)) {
+  const resolvedFile = path107.resolve(file);
+  if (!fs96.existsSync(resolvedFile)) {
     process.exit(0);
   }
   let projectRoot;
   try {
-    projectRoot = findProjectRoot(path106.dirname(resolvedFile));
+    projectRoot = findProjectRoot(path107.dirname(resolvedFile));
   } catch {
     process.exit(0);
   }
   const configResult = await loadConfig(projectRoot);
   if (configResult.isErr()) process.exit(0);
   const config = configResult.value;
-  const dbPath = resolveDbPath5(projectRoot);
+  const dbPath = resolveDbPath6(projectRoot);
   ensureGlobalDirs();
   const db = initializeDatabase(dbPath);
   const store = new Store(db);
@@ -60277,11 +61147,11 @@ program.command("list").description("List all registered projects").option("--js
     console.log("No projects registered. Run `trace-mcp add` in a project directory.");
   } else {
     console.log("Registered projects:\n");
-    for (const p4 of projects) {
-      const lastIdx = p4.lastIndexed ? new Date(p4.lastIndexed).toLocaleString() : "never";
-      const dbExists = fs94.existsSync(p4.dbPath) ? "ok" : "missing";
-      console.log(`  ${p4.name}`);
-      console.log(`    Root: ${p4.root}`);
+    for (const p5 of projects) {
+      const lastIdx = p5.lastIndexed ? new Date(p5.lastIndexed).toLocaleString() : "never";
+      const dbExists = fs96.existsSync(p5.dbPath) ? "ok" : "missing";
+      console.log(`  ${p5.name}`);
+      console.log(`    Root: ${p5.root}`);
       console.log(`    DB: ${dbExists}`);
       console.log(`    Last indexed: ${lastIdx}`);
       console.log();
@@ -60291,11 +61161,13 @@ program.command("list").description("List all registered projects").option("--js
 program.addCommand(initCommand);
 program.addCommand(upgradeCommand);
 program.addCommand(addCommand);
+program.addCommand(removeCommand);
 program.addCommand(doctorCommand);
 program.addCommand(ciReportCommand);
 program.addCommand(checkCommand);
 program.addCommand(bundlesCommand);
 program.addCommand(federationCommand);
 program.addCommand(analyticsCommand);
+program.addCommand(statusCommand);
 program.parse();
 //# sourceMappingURL=cli.js.map