memorix 1.1.8 → 1.1.9

package/CHANGELOG.md

@@ -2,6 +2,15 @@
 
 All notable changes to this project will be documented in this file.
 
+## [1.1.9] - 2026-07-12
+
+### Added
+- **Configurable CodeGraph excludes** -- Added `[codegraph].exclude_patterns` / YAML `codegraph.excludePatterns` support so CodeGraph, Project Context suggested reads, context packs, diagnostics, and related CLI flows can skip project-specific generated or vendor paths while keeping the built-in defaults.
+
+### Fixed
+- **Config inspection aliases** -- `memorix config get` now accepts TOML-style snake_case dotted keys such as `codegraph.exclude_patterns` when reading resolved camelCase config values.
+- **Orama search index consistency** -- Search access tracking now preserves internally stored vector-backed documents, public/detail cache results continue to strip embeddings, and hydration reconciles persisted observations by exact composite ID instead of skipping observation hydration when a shared index already contains mini-skills.
+
 ## [1.1.8] - 2026-07-08
 
 ### Added

package/dist/cli/index.js

@@ -3212,7 +3212,7 @@ ${import_picocolors.default.gray(m3)}  ${s2}
 
 // src/cli/version.ts
 function getCliVersion() {
-  return true ? "1.1.8" : pkg.version;
+  return true ? "1.1.9" : pkg.version;
 }
 var init_version = __esm({
   "src/cli/version.ts"() {
@@ -12429,6 +12429,7 @@ function loadYamlConfig(projectRoot) {
     agent: { ...userConfig.agent, ...projectConfig.agent },
     embedding: { ...userConfig.embedding, ...projectConfig.embedding },
     git: { ...userConfig.git, ...projectConfig.git },
+    codegraph: { ...userConfig.codegraph, ...projectConfig.codegraph },
     behavior: { ...userConfig.behavior, ...projectConfig.behavior },
     server: { ...userConfig.server, ...projectConfig.server },
     team: { ...userConfig.team, ...projectConfig.team }
@@ -12531,6 +12532,7 @@ function mergeTomlConfig(base, override) {
     embedding: { ...base.embedding, ...override.embedding },
     hooks: { ...base.hooks, ...override.hooks },
     git: { ...base.git, ...override.git },
+    codegraph: { ...base.codegraph, ...override.codegraph },
     server: { ...base.server, ...override.server }
   };
 }
@@ -13154,6 +13156,9 @@ function getResolvedConfig(options2 = {}) {
       excludePatterns: firstArray(toml.git?.exclude_patterns, yaml4.git?.excludePatterns),
       noiseKeywords: firstArray(toml.git?.noise_keywords, yaml4.git?.noiseKeywords)
     },
+    codegraph: {
+      excludePatterns: firstArray(toml.codegraph?.exclude_patterns, yaml4.codegraph?.excludePatterns)
+    },
     server: {
       transport: first(toml.server?.transport, yaml4.server?.transport),
       dashboard: firstBool(toml.server?.dashboard, yaml4.server?.dashboard),
@@ -15701,8 +15706,12 @@ function makeEntryKey(projectId, observationId) {
   return `${projectId ?? ""}::${observationId}`;
 }
 function rememberObservationDoc(doc) {
-  if (!doc.projectId || typeof doc.observationId !== "number") return;
-  docByObservationKey.set(makeEntryKey(doc.projectId, doc.observationId), doc);
+  const publicDoc = { ...doc };
+  delete publicDoc.embedding;
+  if (doc.projectId && typeof doc.observationId === "number") {
+    docByObservationKey.set(makeEntryKey(doc.projectId, doc.observationId), publicDoc);
+  }
+  return publicDoc;
 }
 function isCommandLikeQuery(query) {
   return COMMAND_LIKE_QUERY2.test(query);
@@ -15804,14 +15813,14 @@ async function batchGenerateEmbeddings(texts) {
 }
 async function hydrateIndex(observations2) {
   const database = await getDb();
-  const currentCount = await count2(database);
-  if (currentCount > 0) return 0;
   let inserted = 0;
   for (const obs of observations2) {
     if (!obs || !obs.id || !obs.projectId) continue;
     try {
+      const id = makeOramaObservationId(obs.projectId, obs.id);
+      if (getByID(database, id)) continue;
       const doc = {
-        id: makeOramaObservationId(obs.projectId, obs.id),
+        id,
         observationId: obs.id,
         entityName: obs.entityName || "",
         type: obs.type || "discovery",
@@ -15905,6 +15914,7 @@ async function searchObservations(options2) {
   let searchParams = {
     term: originalQuery,
     limit: requestLimit,
+    includeVectors: true,
     ...Object.keys(filters).length > 0 ? { where: filters } : {},
     // Search specific fields (not tokens, accessCount, etc.)
     properties: ["title", "entityName", "narrative", "facts", "concepts", "filesModified"],
@@ -15976,6 +15986,7 @@ async function searchObservations(options2) {
       const vectorOnlyParams = {
         term: "",
         limit: requestLimit,
+        includeVectors: true,
         ...Object.keys(filters).length > 0 ? { where: filters } : {},
         mode: "vector",
         vector: {
@@ -16274,6 +16285,7 @@ async function getObservationsByIds(ids, projectId) {
     }
     const searchResult = await search2(database, {
       term: "",
+      includeVectors: true,
       where: {
         observationId: { eq: id },
         ...projectId ? { projectId } : {}
@@ -16281,7 +16293,7 @@ async function getObservationsByIds(ids, projectId) {
       limit: 1
     });
     if (searchResult.hits.length > 0) {
-      results.push(searchResult.hits[0].document);
+      results.push(rememberObservationDoc(searchResult.hits[0].document));
     }
   }
   return results;
@@ -23258,11 +23270,17 @@ __export(config_get_exports, {
 function readDotted(source, key) {
   let cursor = source;
   for (const part of key.split(".")) {
-    if (!cursor || typeof cursor !== "object" || !(part in cursor)) return void 0;
-    cursor = cursor[part];
+    if (!cursor || typeof cursor !== "object") return void 0;
+    const record2 = cursor;
+    const normalizedPart = part in record2 ? part : snakeToCamel(part);
+    if (!(normalizedPart in record2)) return void 0;
+    cursor = record2[normalizedPart];
   }
   return cursor;
 }
+function snakeToCamel(value) {
+  return value.replace(/_([a-z])/g, (_4, char) => char.toUpperCase());
+}
 function formatValue(value, key) {
   if (typeof value === "string") return shouldRedactKey(key) ? "<redacted>" : value;
   if (typeof value === "number" || typeof value === "boolean") return String(value);
@@ -26289,6 +26307,58 @@ var init_current_facts = __esm({
   }
 });
 
+// src/codegraph/exclude.ts
+function normalizeCodeGraphExcludePatterns(exclude) {
+  return [.../* @__PURE__ */ new Set([
+    ...DEFAULT_CODEGRAPH_EXCLUDES,
+    ...(exclude ?? []).map((pattern) => pattern.trim()).filter(Boolean)
+  ])];
+}
+function isCodeGraphExcludedPath(path29, exclude) {
+  const normalized = normalizeCodePath2(path29);
+  return normalizeCodeGraphExcludePatterns(exclude).some((pattern) => matchesPattern(normalized, normalizeCodePath2(pattern)));
+}
+function normalizeCodePath2(path29) {
+  return path29.replace(/\\/g, "/").replace(/^\.\/+/, "");
+}
+function matchesPattern(path29, pattern) {
+  if (pattern.endsWith("/**")) {
+    const base = pattern.slice(0, -3);
+    if (base.startsWith("**/")) {
+      const suffix = base.slice(3);
+      return path29 === suffix || path29.endsWith(`/${suffix}`) || path29.includes(`/${suffix}/`);
+    }
+    if (!base.includes("/")) {
+      return path29 === base || path29.startsWith(`${base}/`) || path29.includes(`/${base}/`);
+    }
+    return path29 === base || path29.startsWith(`${base}/`);
+  }
+  if (pattern.startsWith("**/")) {
+    const suffix = pattern.slice(3);
+    return path29 === suffix || path29.endsWith(`/${suffix}`);
+  }
+  return path29 === pattern || path29.startsWith(`${pattern}/`);
+}
+var DEFAULT_CODEGRAPH_EXCLUDES;
+var init_exclude = __esm({
+  "src/codegraph/exclude.ts"() {
+    "use strict";
+    init_esm_shims();
+    DEFAULT_CODEGRAPH_EXCLUDES = [
+      "node_modules/**",
+      "dist/**",
+      "build/**",
+      "coverage/**",
+      ".next/**",
+      ".turbo/**",
+      ".git/**",
+      ".tmp/**",
+      ".worktrees/**",
+      ".claude/worktrees/**"
+    ];
+  }
+});
+
 // src/codegraph/lite-provider.ts
 import { createHash as createHash4 } from "crypto";
 import { readdirSync as readdirSync2, readFileSync as readFileSync8, statSync as statSync2 } from "fs";
@@ -26304,18 +26374,6 @@ function languageForPath(path29) {
   const ext = extension(path29);
   return LANGUAGE_BY_EXTENSION.get(ext) ?? "unknown";
 }
-function isExcluded(path29, exclude) {
-  const normalized = normalizeCodePath(path29);
-  return exclude.some((pattern) => {
-    const p2 = normalizeCodePath(pattern);
-    if (p2.endsWith("/**")) {
-      const base = p2.slice(0, -3);
-      return normalized === base || normalized.startsWith(`${base}/`);
-    }
-    if (p2.startsWith("**/")) return normalized.endsWith(p2.slice(3));
-    return normalized === p2 || normalized.startsWith(`${p2}/`);
-  });
-}
 function walk(root, exclude, maxFiles) {
   const out = [];
   const visit = (dir) => {
@@ -26329,7 +26387,7 @@ function walk(root, exclude, maxFiles) {
     for (const entry of entries) {
       const abs = join20(dir, entry.name);
       const rel = normalizeCodePath(relative(root, abs));
-      if (isExcluded(rel, exclude)) continue;
+      if (isCodeGraphExcludedPath(rel, exclude)) continue;
       if (entry.isDirectory()) {
         if (entry.name === ".git" || entry.name === ".worktrees" || entry.name === ".tmp" || entry.name === "node_modules") continue;
         if (rel === ".claude/worktrees" || rel.startsWith(".claude/worktrees/")) continue;
@@ -26417,18 +26475,7 @@ function extractImportEdges(projectId, file, text, indexedAt) {
   return edges;
 }
 async function indexProjectLite(options2) {
-  const exclude = options2.exclude ?? [
-    "node_modules/**",
-    "dist/**",
-    "build/**",
-    "coverage/**",
-    ".next/**",
-    ".turbo/**",
-    ".git/**",
-    ".tmp/**",
-    ".worktrees/**",
-    ".claude/worktrees/**"
-  ];
+  const exclude = normalizeCodeGraphExcludePatterns(options2.exclude);
   const maxFiles = options2.maxFiles ?? 5e3;
   const indexedAt = (/* @__PURE__ */ new Date()).toISOString();
   const paths = walk(options2.projectRoot, exclude, maxFiles);
@@ -26467,6 +26514,7 @@ var init_lite_provider = __esm({
     "use strict";
     init_esm_shims();
     init_ids();
+    init_exclude();
     LANGUAGE_BY_EXTENSION = /* @__PURE__ */ new Map([
       [".ts", "typescript"],
       [".tsx", "typescript"],
@@ -26643,24 +26691,17 @@ function countLanguages(files) {
   }
   return [...counts.entries()].map(([language, files2]) => ({ language, files: files2 })).sort((a3, b3) => a3.language.localeCompare(b3.language));
 }
-function normalizePath2(path29) {
-  return path29.replace(/\\/g, "/");
-}
-function isGeneratedPath(path29) {
-  const normalized = normalizePath2(path29);
-  return /(^|\/)(dist|build|coverage|\.next|\.turbo|node_modules|\.git|\.tmp|\.worktrees)(\/|$)/i.test(normalized) || /(^|\/)\.claude\/worktrees(\/|$)/i.test(normalized);
-}
 function suggestedReadRank(path29) {
-  const normalized = normalizePath2(path29);
+  const normalized = path29.replace(/\\/g, "/");
   if (normalized.startsWith("src/")) return 0;
   if (normalized.startsWith("tests/") || normalized.startsWith("test/")) return 0;
   if (normalized.startsWith("packages/") && normalized.includes("/src/")) return 2;
   return 3;
 }
-function compactSuggestedReads(paths, limit = 8) {
-  return uniq(paths).filter((path29) => !isGeneratedPath(path29)).sort((a3, b3) => suggestedReadRank(a3) - suggestedReadRank(b3)).slice(0, limit);
+function compactSuggestedReads(paths, limit = 8, exclude) {
+  return uniq(paths).filter((path29) => !isCodeGraphExcludedPath(path29, exclude)).sort((a3, b3) => suggestedReadRank(a3) - suggestedReadRank(b3)).slice(0, limit);
 }
-function collectGraph(store2, projectId, observations2) {
+function collectGraph(store2, projectId, observations2, exclude) {
   const files = store2.listFiles(projectId);
   const symbols = files.flatMap((file) => store2.listSymbolsForFile(file.id));
   const filesById = new Map(files.map((file) => [file.id, file]));
@@ -26682,7 +26723,9 @@ function collectGraph(store2, projectId, observations2) {
     freshness[result.status] += 1;
     const observation = observationsById.get(ref.observationId);
     if (!observation) continue;
-    if (result.status === "current" && file) suggestedReads.push(file.path);
+    const excluded = file ? isCodeGraphExcludedPath(file.path, exclude) : false;
+    if (result.status === "current" && file && !excluded) suggestedReads.push(file.path);
+    if (excluded) continue;
     sources.push({
       observationId: observation.id,
       title: observation.title,
@@ -26699,12 +26742,12 @@ function collectGraph(store2, projectId, observations2) {
     refs,
     freshness,
     sources,
-    suggestedReads: compactSuggestedReads(suggestedReads)
+    suggestedReads: compactSuggestedReads(suggestedReads, 8, exclude)
   };
 }
 function buildProjectContextOverview(input) {
   const active = activeObservations(input.observations, input.project.id);
-  const graph = collectGraph(input.store, input.project.id, active);
+  const graph = collectGraph(input.store, input.project.id, active, input.exclude);
   const status = input.store.status(input.project.id);
   return {
     project: input.project,
@@ -26728,7 +26771,7 @@ function buildProjectContextOverview(input) {
 function buildProjectContextExplain(input) {
   const overview = buildProjectContextOverview(input);
   const active = activeObservations(input.observations, input.project.id);
-  const graph = collectGraph(input.store, input.project.id, active);
+  const graph = collectGraph(input.store, input.project.id, active, input.exclude);
   return {
     project: input.project,
     sources: graph.sources.sort((a3, b3) => a3.observationId - b3.observationId || (a3.path ?? "").localeCompare(b3.path ?? "")),
@@ -26782,11 +26825,12 @@ var init_project_context = __esm({
     "use strict";
     init_esm_shims();
     init_freshness2();
+    init_exclude();
   }
 });
 
 // src/codegraph/task-lens.ts
-function normalizePath3(path29) {
+function normalizePath2(path29) {
   return path29.replace(/\\/g, "/");
 }
 function tokenize3(text) {
@@ -26816,7 +26860,7 @@ function resolveTaskLens(task) {
   return best.score > 0 ? LENSES[best.id] : LENSES.general;
 }
 function pathKindScore(path29, lens) {
-  const normalized = normalizePath3(path29).toLowerCase();
+  const normalized = normalizePath2(path29).toLowerCase();
   const name = normalized.split("/").pop() ?? normalized;
   const inDocs = normalized.startsWith("docs/") || name === "readme.md" || name.includes("readme");
   const isTest = /(^|\/)(tests?|__tests__|spec|fixtures?)\//.test(normalized) || /\.(test|spec)\.[cm]?[jt]sx?$/.test(normalized) || /\.(test|spec)\.py$/.test(normalized);
@@ -26865,7 +26909,7 @@ function sourceTaskMatchScore(source, task) {
   return 0;
 }
 function fallbackPathRank(path29) {
-  const normalized = normalizePath3(path29);
+  const normalized = normalizePath2(path29);
   if (normalized.startsWith("src/")) return 0;
   if (normalized.startsWith("tests/") || normalized.startsWith("test/")) return 1;
   if (normalized.startsWith("packages/") && normalized.includes("/src/")) return 2;
@@ -26874,7 +26918,7 @@ function fallbackPathRank(path29) {
 }
 function rankLensPaths(paths, lens, task) {
   const tokens = tokenize3(task ?? "");
-  return [...new Set(paths.map(normalizePath3))].map((path29, index) => ({
+  return [...new Set(paths.map(normalizePath2))].map((path29, index) => ({
     path: path29,
     index,
     score: pathKindScore(path29, lens) + tokenScore(path29, tokens),
@@ -27128,6 +27172,7 @@ async function buildAutoProjectContext(input) {
   const now = input.now ?? /* @__PURE__ */ new Date();
   const task = input.task?.trim();
   const lens = resolveTaskLens(task);
+  const exclude = input.exclude ?? getResolvedConfig({ projectRoot: input.project.rootPath }).codegraph.excludePatterns;
   const store2 = new CodeGraphStore();
   await store2.init(input.dataDir);
   const initialStatus = store2.status(input.project.id);
@@ -27145,7 +27190,8 @@ async function buildAutoProjectContext(input) {
     try {
       const indexed = await indexProjectLite({
         projectId: input.project.id,
-        projectRoot: input.project.rootPath
+        projectRoot: input.project.rootPath,
+        exclude
       });
       store2.replaceProjectIndex(input.project.id, indexed);
       const backfill = await backfillMissingObservationCodeRefs(
@@ -27165,12 +27211,14 @@ async function buildAutoProjectContext(input) {
   const overview = buildProjectContextOverview({
     project: input.project,
     store: store2,
-    observations: input.observations
+    observations: input.observations,
+    exclude
   });
   const explain = buildProjectContextExplain({
     project: input.project,
     store: store2,
-    observations: input.observations
+    observations: input.observations,
+    exclude
   });
   return {
     project: input.project,
@@ -27380,6 +27428,7 @@ var init_auto_context = __esm({
   "src/codegraph/auto-context.ts"() {
     "use strict";
     init_esm_shims();
+    init_resolved_config();
     init_binder();
     init_current_facts();
     init_lite_provider();
@@ -27516,10 +27565,6 @@ function tokenize4(text) {
 function timestampOf(observation) {
   return Date.parse(observation.updatedAt ?? observation.createdAt ?? "") || 0;
 }
-function isGeneratedPath2(path29) {
-  const normalized = path29.replace(/\\/g, "/");
-  return /(^|\/)(dist|build|coverage|\.next|\.turbo|node_modules|\.git|\.tmp|\.worktrees)(\/|$)/i.test(normalized) || /(^|\/)\.claude\/worktrees(\/|$)/i.test(normalized);
-}
 function relevanceScore(observation, taskTokens) {
   if (taskTokens.length === 0) return 0;
   const title = observation.title.toLowerCase();
@@ -27570,7 +27615,8 @@ function assembleContextPackForTask(input) {
     refs,
     files,
     symbols,
-    suggestedVerification: input.suggestedVerification
+    suggestedVerification: input.suggestedVerification,
+    exclude: input.exclude
   });
 }
 function assembleContextPack(input) {
@@ -27589,6 +27635,7 @@ function assembleContextPack(input) {
     observationIdsWithRefs.add(ref.observationId);
     const file = ref.fileId ? files.get(ref.fileId) : void 0;
     const symbol = ref.symbolId ? symbols.get(ref.symbolId) : void 0;
+    if (file && isCodeGraphExcludedPath(file.path, input.exclude)) continue;
     const freshness = evaluateCodeRefFreshness(ref, file, symbol);
     if (freshness.status === "current") {
       const memoryKey = `${observation.id}:${freshness.status}`;
@@ -27654,8 +27701,8 @@ function buildContextPackPrompt(pack) {
   const reliableMemories = pack.memories.filter((memory) => memory.status === "current");
   const unboundMemories = pack.memories.filter((memory) => memory.status === "unbound");
   const lines = ["## Task", pack.task, "", "## Reliable Memories"];
-  const visibleCodeFacts = pack.codeFacts.filter((fact) => !isGeneratedPath2(fact.path)).slice(0, 5);
-  const visibleSuggestedReads = pack.suggestedReads.filter((path29) => !isGeneratedPath2(path29)).slice(0, 5);
+  const visibleCodeFacts = pack.codeFacts.filter((fact) => !isCodeGraphExcludedPath(fact.path)).slice(0, 5);
+  const visibleSuggestedReads = pack.suggestedReads.filter((path29) => !isCodeGraphExcludedPath(path29)).slice(0, 5);
   if (reliableMemories.length === 0) lines.push("- none");
   for (const memory of reliableMemories) {
     lines.push(`- #${memory.id} ${memory.status}: [${memory.type}] ${memory.title} (${memory.reason})`);
@@ -27690,6 +27737,7 @@ var init_context_pack = __esm({
     "use strict";
     init_esm_shims();
     init_freshness2();
+    init_exclude();
   }
 });
 
@@ -27728,6 +27776,7 @@ var init_codegraph = __esm({
     init_lite_provider();
     init_context_pack();
     init_binder();
+    init_resolved_config();
     init_observations();
     init_operator_shared();
     codegraph_default = defineCommand({
@@ -27750,6 +27799,7 @@ var init_codegraph = __esm({
           const store2 = new CodeGraphStore();
           await store2.init(dataDir);
           const explicitAction = Boolean(positional[0] || args.action);
+          const exclude = getResolvedConfig({ projectRoot: project.rootPath }).codegraph.excludePatterns;
           switch (action) {
             case "status": {
               const status = store2.status(project.id);
@@ -27762,7 +27812,8 @@ ${formatUsageHint()}`;
             case "refresh": {
               const indexed = await indexProjectLite({
                 projectId: project.id,
-                projectRoot: project.rootPath
+                projectRoot: project.rootPath,
+                exclude
               });
               store2.replaceProjectIndex(project.id, indexed);
               const activeObservations2 = getAllObservations().filter((obs) => obs.projectId === project.id && (obs.status ?? "active") === "active");
@@ -27793,7 +27844,8 @@ ${formatUsageHint()}`;
                 projectId: project.id,
                 task,
                 observations: observations2,
-                limit
+                limit,
+                exclude
               });
               emitResult({ project, pack }, buildContextPackPrompt(pack), asJson);
               return;
@@ -61964,7 +62016,7 @@ The path should point to a directory containing a .git folder.`
   };
   const server = existingServer ?? new McpServer({
     name: "memorix",
-    version: true ? "1.1.8" : "1.0.1"
+    version: true ? "1.1.9" : "1.0.1"
   });
   const originalRegisterTool = server.registerTool.bind(server);
   server.registerTool = ((name, ...args) => {
@@ -62666,15 +62718,18 @@ _Search mode: ${getLastSearchMode2(project.id)}_`;
       return withFreshIndex(async () => {
         const { CodeGraphStore: CodeGraphStore2 } = await Promise.resolve().then(() => (init_store(), store_exports));
         const { assembleContextPackForTask: assembleContextPackForTask2, buildContextPackPrompt: buildContextPackPrompt2 } = await Promise.resolve().then(() => (init_context_pack(), context_pack_exports));
+        const { getResolvedConfig: getResolvedConfig2 } = await Promise.resolve().then(() => (init_resolved_config(), resolved_config_exports));
         const store2 = new CodeGraphStore2();
         await store2.init(projectDir2);
+        const exclude = getResolvedConfig2({ projectRoot: project.rootPath }).codegraph.excludePatterns;
         const observations2 = getAllObservations().filter((obs) => obs.projectId === project.id && (obs.status ?? "active") === "active").reverse();
         const pack = assembleContextPackForTask2({
           store: store2,
           projectId: project.id,
           task,
           observations: observations2,
-          limit: typeof limit === "number" ? limit : 20
+          limit: typeof limit === "number" ? limit : 20,
+          exclude
         });
         const text = buildContextPackPrompt2(pack);
         return {
@@ -71470,7 +71525,7 @@ function getMemorixDir() {
   const home = process.env.HOME || process.env.USERPROFILE || "";
   return home.replace(/\\/g, "/") + "/.memorix";
 }
-function normalizePath4(p2) {
+function normalizePath3(p2) {
   return process.platform === "win32" ? p2.replace(/\//g, "\\") : p2;
 }
 function getStateFilePath() {
@@ -71636,7 +71691,7 @@ async function doStart(port) {
     `  Port:       ${port}`,
     `  Dashboard:  http://127.0.0.1:${port}/`,
     `  MCP:        http://127.0.0.1:${port}/mcp`,
-    `  Logs:       ${normalizePath4(logFile)}`,
+    `  Logs:       ${normalizePath3(logFile)}`,
     ""
   ].join("\n");
   process.stderr.write(startMsg + "\n");
@@ -71650,7 +71705,7 @@ async function doStart(port) {
     }
     if (!isProcessRunning(pid)) {
       console.error("[ERROR] Background process exited unexpectedly.");
-      console.error(`  Check logs: ${normalizePath4(logFile)}`);
+      console.error(`  Check logs: ${normalizePath3(logFile)}`);
       clearState();
       process.exitCode = 1;
       return;
@@ -71788,7 +71843,7 @@ async function doStatus() {
   if (state.instanceToken) console.log(`  Instance:   ${state.instanceToken.slice(0, 8)}\u2026`);
   console.log(`  Dashboard:  http://127.0.0.1:${state.port}/`);
   console.log(`  MCP:        http://127.0.0.1:${state.port}/mcp`);
-  console.log(`  Logs:       ${normalizePath4(state.logFile)}`);
+  console.log(`  Logs:       ${normalizePath3(state.logFile)}`);
   if (health.ok && health.data) {
     const d3 = health.data;
     console.log("");
@@ -72759,8 +72814,10 @@ var init_doctor = __esm({
           try {
             const { CodeGraphStore: CodeGraphStore2 } = await Promise.resolve().then(() => (init_store(), store_exports));
             const { buildProjectContextOverview: buildProjectContextOverview2 } = await Promise.resolve().then(() => (init_project_context(), project_context_exports));
+            const { getResolvedConfig: getResolvedConfig2 } = await Promise.resolve().then(() => (init_resolved_config(), resolved_config_exports));
             const codeStore = new CodeGraphStore2();
             await codeStore.init(dataDir);
+            const exclude = getResolvedConfig2({ projectRoot: projectRoot || process.cwd() }).codegraph.excludePatterns;
             const overview = buildProjectContextOverview2({
               project: {
                 id: projectId,
@@ -72768,7 +72825,8 @@ var init_doctor = __esm({
                 rootPath: projectRoot || process.cwd()
               },
               store: codeStore,
-              observations: projectObservations
+              observations: projectObservations,
+              exclude
             });
             const languageText = overview.code.languages.length > 0 ? overview.code.languages.map((item) => `${item.language} ${item.files}`).join(", ") : "none indexed yet";
             if (overview.code.files > 0) {
@@ -74826,8 +74884,8 @@ function buildIdleReasons(available, dispatchedNames, config2, excludeAgents) {
   const excluded = excludeAgents ?? /* @__PURE__ */ new Set();
   for (const adapter of available) {
     if (dispatchedNames.has(adapter.name)) continue;
-    const isExcluded2 = excluded.has(adapter.name);
-    if (isExcluded2) {
+    const isExcluded = excluded.has(adapter.name);
+    if (isExcluded) {
       result.push({ name: adapter.name, reason: "excluded due to prior failure" });
     } else {
       const inAnyPref = Object.values(DEFAULT_ROLE_PREFERENCES).some((prefs) => prefs.includes(adapter.name));