trace-mcp 1.6.1 → 1.8.0

package/dist/index.js

@@ -4,10 +4,16 @@ var __getOwnPropDesc = Object.getOwnPropertyDescriptor;
 var __getOwnPropNames = Object.getOwnPropertyNames;
 var __getProtoOf = Object.getPrototypeOf;
 var __hasOwnProp = Object.prototype.hasOwnProperty;
+var __require = /* @__PURE__ */ ((x) => typeof require !== "undefined" ? require : typeof Proxy !== "undefined" ? new Proxy(x, {
+  get: (a, b) => (typeof require !== "undefined" ? require : a)[b]
+}) : x)(function(x) {
+  if (typeof require !== "undefined") return require.apply(this, arguments);
+  throw Error('Dynamic require of "' + x + '" is not supported');
+});
 var __esm = (fn, res) => function __init() {
   return fn && (res = (0, fn[__getOwnPropNames(fn)[0]])(fn = 0)), res;
 };
-var __commonJS = (cb, mod) => function __require() {
+var __commonJS = (cb, mod) => function __require2() {
   return mod || (0, cb[__getOwnPropNames(cb)[0]])((mod = { exports: {} }).exports, mod), mod.exports;
 };
 var __export = (target, all) => {
@@ -1106,7 +1112,7 @@ var require_parse = __commonJS({
       }
       return { risky: false };
     };
-    var parse = (input, options) => {
+    var parse2 = (input, options) => {
       if (typeof input !== "string") {
         throw new TypeError("Expected a string");
       }
@@ -1276,7 +1282,7 @@ var require_parse = __commonJS({
             output = token.close = `)$))${extglobStar}`;
           }
           if (token.inner.includes("*") && (rest = remaining()) && /^\.[^\\/.]+$/.test(rest)) {
-            const expression = parse(rest, { ...options, fastpaths: false }).output;
+            const expression = parse2(rest, { ...options, fastpaths: false }).output;
             output = token.close = `)${expression})${extglobStar})`;
           }
           if (token.prev.type === "bos") {
@@ -1798,7 +1804,7 @@ var require_parse = __commonJS({
       }
       return state;
     };
-    parse.fastpaths = (input, options) => {
+    parse2.fastpaths = (input, options) => {
       const opts = { ...options };
       const max = typeof opts.maxLength === "number" ? Math.min(MAX_LENGTH, opts.maxLength) : MAX_LENGTH;
       const len = input.length;
@@ -1863,7 +1869,7 @@ var require_parse = __commonJS({
       }
       return source;
     };
-    module.exports = parse;
+    module.exports = parse2;
   }
 });
 
@@ -1872,7 +1878,7 @@ var require_picomatch = __commonJS({
   "node_modules/picomatch/lib/picomatch.js"(exports, module) {
     "use strict";
     var scan = require_scan();
-    var parse = require_parse();
+    var parse2 = require_parse();
     var utils = require_utils();
     var constants = require_constants();
     var isObject = (val) => val && typeof val === "object" && !Array.isArray(val);
@@ -1960,7 +1966,7 @@ var require_picomatch = __commonJS({
     picomatch3.isMatch = (str2, patterns, options) => picomatch3(patterns, options)(str2);
     picomatch3.parse = (pattern, options) => {
       if (Array.isArray(pattern)) return pattern.map((p) => picomatch3.parse(p, options));
-      return parse(pattern, { ...options, fastpaths: false });
+      return parse2(pattern, { ...options, fastpaths: false });
     };
     picomatch3.scan = (input, options) => scan(input, options);
     picomatch3.compileRe = (state, options, returnOutput = false, returnState = false) => {
@@ -1986,10 +1992,10 @@ var require_picomatch = __commonJS({
       }
       let parsed = { negated: false, fastpaths: true };
       if (options.fastpaths !== false && (input[0] === "." || input[0] === "*")) {
-        parsed.output = parse.fastpaths(input, options);
+        parsed.output = parse2.fastpaths(input, options);
       }
       if (!parsed.output) {
-        parsed = parse(input, options);
+        parsed = parse2(input, options);
       }
       return picomatch3.compileRe(parsed, options, returnOutput, returnState);
     };
@@ -3644,7 +3650,7 @@ function captureGraphSnapshots(store, cwd) {
 
 // src/db/schema.ts
 import Database from "better-sqlite3";
-var SCHEMA_VERSION = 16;
+var SCHEMA_VERSION = 17;
 var DDL = `
 -- ============================================================
 -- UNIFIED ADDRESS SPACE
@@ -4525,6 +4531,25 @@ 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) {
@@ -5892,16 +5917,18 @@ 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;
@@ -5986,6 +6013,13 @@ 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();
@@ -6032,6 +6066,8 @@ 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());
@@ -6057,6 +6093,11 @@ 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;
   }
@@ -7297,8 +7338,170 @@ var GLOBAL_CONFIG_PATH = path12.join(TRACE_MCP_HOME, ".config.json");
 var INDEX_DIR = path12.join(TRACE_MCP_HOME, "index");
 var REGISTRY_PATH = path12.join(TRACE_MCP_HOME, "registry.json");
 var TOPOLOGY_DB_PATH = path12.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": "gemma4-e4b",             // ollama: "gemma4-e4b", openai: "gpt-4o-mini"
+    "fast_model": "gemma4-e4b",                  // ollama: "gemma4-e4b", openai: "gpt-4o-mini"
+    "embedding_model": "qwen3-embedding:0.6b",   // 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() {
   fs11.mkdirSync(INDEX_DIR, { recursive: true });
+  if (!fs11.existsSync(GLOBAL_CONFIG_PATH)) {
+    fs11.writeFileSync(GLOBAL_CONFIG_PATH, DEFAULT_CONFIG_JSONC);
+  }
 }
 function projectHash(absolutePath) {
   return crypto2.createHash("sha256").update(absolutePath).digest("hex").slice(0, 12);
@@ -8605,10 +8808,13 @@ 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) }] };
     }
   );
@@ -9788,10 +9994,34 @@ var DEFAULT_WEIGHTS = { primary: 0.4, dependencies: 0.3, callers: 0.2, typeConte
 function assembleStructuredContext(request) {
   const weights = request.budgetWeights ?? DEFAULT_WEIGHTS;
   const budget = request.totalBudget;
-  const primaryResult = assembleContext(request.primary, Math.floor(budget * weights.primary));
-  const depsResult = assembleContext(request.dependencies, Math.floor(budget * weights.dependencies));
-  const callersResult = assembleContext(request.callers, Math.floor(budget * weights.callers));
-  const typeResult = assembleContext(request.typeContext, Math.floor(budget * weights.typeContext));
+  const categories = ["primary", "dependencies", "callers", "typeContext"];
+  const itemCounts = {
+    primary: request.primary.length,
+    dependencies: request.dependencies.length,
+    callers: request.callers.length,
+    typeContext: request.typeContext.length
+  };
+  let surplusWeight = 0;
+  let activeWeight = 0;
+  for (const cat of categories) {
+    if (itemCounts[cat] === 0) {
+      surplusWeight += weights[cat];
+    } else {
+      activeWeight += weights[cat];
+    }
+  }
+  const effectiveWeights = { primary: 0, dependencies: 0, callers: 0, typeContext: 0 };
+  for (const cat of categories) {
+    if (itemCounts[cat] === 0) {
+      effectiveWeights[cat] = 0;
+    } else if (activeWeight > 0) {
+      effectiveWeights[cat] = weights[cat] + surplusWeight * (weights[cat] / activeWeight);
+    }
+  }
+  const primaryResult = assembleContext(request.primary, Math.floor(budget * effectiveWeights.primary));
+  const depsResult = assembleContext(request.dependencies, Math.floor(budget * effectiveWeights.dependencies));
+  const callersResult = assembleContext(request.callers, Math.floor(budget * effectiveWeights.callers));
+  const typeResult = assembleContext(request.typeContext, Math.floor(budget * effectiveWeights.typeContext));
   return {
     primary: primaryResult.items,
     dependencies: depsResult.items,
@@ -9834,19 +10064,34 @@ var CALL_EDGES = /* @__PURE__ */ new Set([
   "nest_injects",
   "graphql_resolves"
 ]);
-function readSource(sym, file, rootPath) {
-  try {
-    const absPath = path22.resolve(rootPath, file.path);
-    return readByteRange(absPath, sym.byte_start, sym.byte_end, !!file.gitignored) ?? void 0;
-  } catch {
-    return void 0;
+var FileReadCache = class {
+  constructor(rootPath) {
+    this.rootPath = rootPath;
   }
-}
-function toContextItem(sym, file, rootPath, score) {
+  rootPath;
+  cache = /* @__PURE__ */ new Map();
+  readSymbolSource(sym, file) {
+    let buf = this.cache.get(file.id);
+    if (buf === void 0) {
+      try {
+        const absPath = path22.resolve(this.rootPath, file.path);
+        const fs39 = __require("fs");
+        buf = fs39.readFileSync(absPath);
+      } catch {
+        buf = null;
+      }
+      this.cache.set(file.id, buf);
+    }
+    if (!buf || sym.byte_start == null || sym.byte_end == null) return void 0;
+    if (file.gitignored) return "[gitignored]";
+    return buf.subarray(sym.byte_start, sym.byte_end).toString("utf-8");
+  }
+};
+function toContextItemCached(sym, file, cache, score, signatureOnly) {
   return {
     id: sym.symbol_id,
     score,
-    source: readSource(sym, file, rootPath),
+    source: signatureOnly ? void 0 : cache.readSymbolSource(sym, file),
     signature: sym.signature ?? void 0,
     metadata: `[${sym.kind}] ${sym.fqn ?? sym.name} \u2014 ${file.path}`
   };
@@ -9957,14 +10202,16 @@ function getContextBundle(store, rootPath, opts) {
       }
     }
   }
+  const fileCache = new FileReadCache(rootPath);
   const primaryItems = primarySymbols.map(
-    (p, i) => toContextItem(p.sym, p.file, rootPath, 1 - i * 0.01)
+    (p, i) => toContextItemCached(p.sym, p.file, fileCache, 1 - i * 0.01, false)
   );
+  const MAX_FULL_SOURCE_DEPS = 10;
   const depItems = depSymbols.map(
-    (d, i) => toContextItem(d.sym, d.file, rootPath, 0.8 - i * 5e-3)
+    (d, i) => toContextItemCached(d.sym, d.file, fileCache, 0.8 - i * 5e-3, i >= MAX_FULL_SOURCE_DEPS)
   );
   const callerItems = callerSymbols.map(
-    (c, i) => toContextItem(c.sym, c.file, rootPath, 0.6 - i * 5e-3)
+    (c, i) => toContextItemCached(c.sym, c.file, fileCache, 0.6 - i * 5e-3, i >= MAX_FULL_SOURCE_DEPS)
   );
   const assembled = assembleStructuredContext({
     primary: primaryItems,
@@ -11428,7 +11675,7 @@ function detectFramework(allFiles) {
   }
   return "unknown";
 }
-function readSource2(rootPath, filePath) {
+function readSource(rootPath, filePath) {
   try {
     return fs20.readFileSync(path26.resolve(rootPath, filePath), "utf-8");
   } catch {
@@ -11440,7 +11687,7 @@ function buildExpressChain(store, rootPath, url, allFiles, chain) {
   const PATH_MW_RE = /(?:app|router)\s*\.\s*use\s*\(\s*['"`]([^'"`]+)['"`]\s*,\s*([A-Za-z][\w.]*)/g;
   for (const file of allFiles) {
     if (file.framework_role !== "express_router" && file.framework_role !== "express_middleware") continue;
-    const source = readSource2(rootPath, file.path);
+    const source = readSource(rootPath, file.path);
     if (!source) continue;
     let match;
     const globalRe = new RegExp(GLOBAL_MW_RE.source, "g");
@@ -11465,7 +11712,7 @@ function buildNestChain(store, rootPath, route, allFiles, chain) {
   const FILTERS_RE = /@UseFilters\(\s*([^)]+)\s*\)/g;
   const controllerFiles = allFiles.filter((f) => f.framework_role === "nest_controller");
   for (const file of controllerFiles) {
-    const source = readSource2(rootPath, file.path);
+    const source = readSource(rootPath, file.path);
     if (!source) continue;
     const extractDecorators = (regex, scope) => {
       const re = new RegExp(regex.source, "g");
@@ -11518,7 +11765,7 @@ function buildFlaskChain(store, rootPath, url, allFiles, chain) {
   }
   for (const file of allFiles) {
     if (file.framework_role !== "flask_routes") continue;
-    const source = readSource2(rootPath, file.path);
+    const source = readSource(rootPath, file.path);
     if (!source) continue;
     const decoratorRe = /@([\w.]+)\s*(?:\([^)]*\))?\s*\n\s*(?:@\w[\w.]*\s*(?:\([^)]*\))?\s*\n\s*)*def\s+\w+/g;
     let m;
@@ -11533,7 +11780,7 @@ function buildFlaskChain(store, rootPath, url, allFiles, chain) {
 function buildFastAPIChain(store, rootPath, url, allFiles, chain) {
   for (const file of allFiles) {
     if (file.framework_role !== "fastapi_routes" && file.framework_role !== "fastapi_app") continue;
-    const source = readSource2(rootPath, file.path);
+    const source = readSource(rootPath, file.path);
     if (!source) continue;
     const addMwRe = /(?:app|router)\s*\.\s*add_middleware\s*\(\s*([\w.]+)/g;
     let m;
@@ -11561,7 +11808,7 @@ function buildFastAPIChain(store, rootPath, url, allFiles, chain) {
 function buildDjangoChain(store, rootPath, allFiles, chain) {
   for (const file of allFiles) {
     if (!file.path.endsWith("settings.py") && !file.path.includes("settings/")) continue;
-    const source = readSource2(rootPath, file.path);
+    const source = readSource(rootPath, file.path);
     if (!source) continue;
     const mwMatch = source.match(/MIDDLEWARE\s*=\s*\[([\s\S]*?)\]/);
     if (!mwMatch) continue;
@@ -11575,7 +11822,7 @@ function buildDjangoChain(store, rootPath, allFiles, chain) {
   }
   for (const file of allFiles) {
     if (file.framework_role !== "view") continue;
-    const source = readSource2(rootPath, file.path);
+    const source = readSource(rootPath, file.path);
     if (!source) continue;
     const decoratorRe = /@([\w.]+)\s*(?:\([^)]*\))?\s*\n\s*(?:@\w[\w.]*\s*(?:\([^)]*\))?\s*\n\s*)*(?:def|class)\s+\w+/g;
     let m;
@@ -26606,6 +26853,98 @@ 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 perCallHintsOverhead = group.length * 120;
+    const bl = estimateTokens3(totalSourceBytes + importOverhead) + perCallHintsOverhead;
+    const tm = estimateTokens3(Math.round((totalSourceBytes + importOverhead) * 0.45));
+    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 perCallFramingOverhead = 150;
+    const perCallHintsOverhead = 120;
+    const perCallMetadataOverhead = 40;
+    const perCallOverhead = perCallFramingOverhead + perCallHintsOverhead + perCallMetadataOverhead;
+    const contentTokens = group.reduce((s, sym) => s + estimateTokens3(sym.source_bytes || 200), 0);
+    const bl = contentTokens + batchSize * perCallOverhead;
+    const tm = contentTokens + perCallFramingOverhead;
+    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);
@@ -26615,8 +26954,13 @@ 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);
@@ -27184,11 +27528,11 @@ 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("");
@@ -27227,10 +27571,10 @@ 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: [] });
@@ -27313,7 +27657,7 @@ 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, {
@@ -27394,11 +27738,11 @@ 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("");
@@ -27721,7 +28065,14 @@ function registerSessionTools(server, ctx) {
           const text = response.content?.[0]?.text;
           if (text) {
             try {
-              results.push({ tool: call.tool, result: JSON.parse(text) });
+              const parsed = JSON.parse(text);
+              if (parsed && typeof parsed === "object") {
+                delete parsed._hints;
+                delete parsed._optimization_hint;
+                delete parsed._budget_warning;
+                delete parsed._budget_level;
+              }
+              results.push({ tool: call.tool, result: parsed });
             } catch {
               results.push({ tool: call.tool, result: text });
             }
@@ -27739,7 +28090,7 @@ function registerSessionTools(server, ctx) {
 }
 
 // src/server/server.ts
-var PKG_VERSION = true ? "1.6.1" : "0.0.0-dev";
+var PKG_VERSION = true ? "1.8.0" : "0.0.0-dev";
 function j2(value) {
   return JSON.stringify(value, (_key, val) => val === null || val === void 0 ? void 0 : val);
 }
@@ -27843,7 +28194,7 @@ 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((p) => p.manifest.name)
@@ -27990,7 +28341,8 @@ function createServer2(store, registry, config, rootPath) {
     guardPath,
     j: j2,
     jh,
-    markExplored: explored.markExplored
+    markExplored: explored.markExplored,
+    progress: progress ?? null
   };
   const metaCtx = {
     ...ctx,
@@ -28272,6 +28624,24 @@ 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(",");
@@ -28951,6 +29321,12 @@ 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);
   }
@@ -29205,7 +29581,13 @@ var PluginRegistry = class {
 // src/config.ts
 import { cosmiconfig } from "cosmiconfig";
 import { z as z13 } from "zod";
+import fs38 from "fs";
+
+// src/config-jsonc.ts
 import fs37 from "fs";
+import { modify, applyEdits, parse } from "jsonc-parser";
+
+// src/config.ts
 var SecurityConfigSchema = z13.object({
   secret_patterns: z13.array(z13.string()).optional(),
   max_file_size_bytes: z13.number().positive().optional(),
@@ -29408,9 +29790,9 @@ var TraceMcpConfigSchema = z13.object({
   children: z13.array(z13.string()).optional()
 });
 function loadGlobalConfigRaw() {
-  if (!fs37.existsSync(GLOBAL_CONFIG_PATH)) return {};
+  if (!fs38.existsSync(GLOBAL_CONFIG_PATH)) return {};
   try {
-    return JSON.parse(fs37.readFileSync(GLOBAL_CONFIG_PATH, "utf-8"));
+    return JSON.parse(stripJsonComments(fs38.readFileSync(GLOBAL_CONFIG_PATH, "utf-8")));
   } catch {
     return {};
   }