@mnemonik/shared 6.2.8 → 6.3.0

package/dist/FileSystemReader.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"FileSystemReader.d.ts","sourceRoot":"","sources":["../src/FileSystemReader.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAOH,OAAO,EAAe,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAqE1D,MAAM,WAAW,QAAQ;IACvB,sCAAsC;IACtC,IAAI,EAAE,MAAM,CAAC;IACb,4CAA4C;IAC5C,IAAI,EAAE,MAAM,CAAC;CACd;AAED,MAAM,WAAW,eAAe;IAC9B,KAAK,EAAE,QAAQ,EAAE,CAAC;IAClB,MAAM,EAAE,SAAS,EAAE,CAAC;CACrB;AAED,MAAM,WAAW,kBAAkB;IACjC,OAAO,EAAE,QAAQ,EAAE,CAAC;IACpB,MAAM,EAAE,SAAS,EAAE,CAAC;IACpB,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,qBAAa,gBAAgB;IAC3B;;;OAGG;IACG,gBAAgB,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAM1D;;;OAGG;IACG,iBAAiB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;IAiC1D;;OAEG;IACG,aAAa,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,eAAe,CAAC;IAoBlE;;;OAGG;IACG,kBAAkB,CACtB,WAAW,EAAE,MAAM,EACnB,WAAW,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAC/B,OAAO,CAAC,kBAAkB,CAAC;IA0C9B;;OAEG;IACG,eAAe,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC;IAY/D;;OAEG;IACG,QAAQ,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC;QAAE,KAAK,EAAE,IAAI,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,GAAG,IAAI,CAAC;YAejE,iBAAiB;IAqC/B,OAAO,CAAC,UAAU;CAKnB;AAID,wBAAgB,mBAAmB,IAAI,gBAAgB,CAGtD"}

package/dist/FileSystemReader.js

@@ -14,6 +14,11 @@ import { withTimeout } from './asyncUtils.js';
 import { CodeScanner } from './codeScanner.js';
 const FILE_OP_TIMEOUT_MS = 5000;
 const MAX_FILE_SIZE = 10 * 1024 * 1024; // 10 MB
+// NOTE: this SKIP_DIRS is NOT an index gate — FileSystemReader's walk methods
+// (scanDirectory/detectChangedFiles) have no live caller; only readFileContent
+// (single file, no ignore) is used, for JIT citation verification. The
+// authoritative built-in list is BUILT_IN_IGNORE_DIRS in codeScanner.ts. Left
+// as-is (dead) rather than rewired to avoid churn on unused code.
 const SKIP_DIRS = new Set([
     'node_modules',
     '.git',

package/dist/FileSystemReader.js.map

@@ -1 +1 @@
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package/dist/codeScanner.d.ts

@@ -23,6 +23,17 @@ export interface ScanOptions {
     ignorePatterns?: string[];
     includeExtensions?: string[];
 }
+/**
+ * Directory basenames the scanner never indexes, across every ecosystem —
+ * generated output, package-manager/build caches, and vendored deps. SINGLE
+ * SOURCE OF TRUTH: the scanner package's discovery + watch walks import this
+ * (`packages/scanner/src/{discovery,watcher}.ts`) and `src/core/utils.ts`
+ * derives from it, so every ignore surface agrees instead of drifting (the
+ * pre-2026-07 state had four divergent copies). Add only UNAMBIGUOUS names —
+ * a project's own `.gitignore` / `.mnemonikignore` covers the ambiguous,
+ * project-specific cases (`vendor/`, custom dirs) hierarchically.
+ */
+export declare const BUILT_IN_IGNORE_DIRS: readonly string[];
 /**
  * Matchers for authority manifest / config / CI files whose verbatim content
  * is collected by `collectAuthorityFiles` and pushed to the server for
@@ -54,6 +65,29 @@ export declare function isGitBoundary(dirPath: string): Promise<boolean>;
 export declare class CodeScanner {
     private options;
     constructor(options?: ScanOptions);
+    /**
+     * Read `.gitignore` + `.mnemonikignore` in `absDir` and compile them into one
+     * ignore layer (the two files are unioned — `.mnemonikignore` is just an
+     * additional gitignore-syntax exclusion list). Returns null when neither file
+     * exists. FAIL-CLOSED: a non-ENOENT read error (EISDIR, EACCES, timeout)
+     * latches `walk.complete = false` so callers deriving *removals* from the walk
+     * treat it as untrustworthy rather than silently ignoring nothing.
+     */
+    private loadIgnoreLayer;
+    /**
+     * True when `entryRel` (relative to the scan root) is excluded by any ignore
+     * layer in `stack`. Tested deepest-first: the first layer that explicitly
+     * ignores OR re-includes (via a `!negation`) wins, matching git's rule that a
+     * deeper `.gitignore` overrides a shallower one. Directories are tested with a
+     * trailing slash so `foo/` dir-only rules match the directory itself.
+     */
+    private ignoredByStack;
+    /**
+     * Reconstruct the root→parent ignore-layer stack for a single file, for the
+     * incremental `scanFiles` path (which has a flat file list, not a recursive
+     * walk). Layers are memoized per directory in `cache` across a batch.
+     */
+    private buildIgnoreStackForFile;
     /**
      * True when any directory strictly between `rootPath` and `filePath`
      * carries its own `.git` entry (see isGitBoundary). Paths that don't

package/dist/codeScanner.d.ts.map

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package/dist/codeScanner.js

@@ -4,6 +4,7 @@
 import { readdir, readFile, stat, lstat, realpath } from 'fs/promises';
 import { join, relative, extname, sep } from 'path';
 import { createHash } from 'crypto';
+import ignore from 'ignore';
 import { debug as logDebug } from './logger.js';
 import { withTimeout } from './asyncUtils.js';
 import { scrubSecrets } from './secretPatterns.js';
@@ -11,69 +12,97 @@ import { scrubSecrets } from './secretPatterns.js';
  * File operation timeout (5 seconds) to prevent hanging on slow/unresponsive filesystems
  */
 const FILE_OP_TIMEOUT_MS = 5000;
+/**
+ * Directory basenames the scanner never indexes, across every ecosystem —
+ * generated output, package-manager/build caches, and vendored deps. SINGLE
+ * SOURCE OF TRUTH: the scanner package's discovery + watch walks import this
+ * (`packages/scanner/src/{discovery,watcher}.ts`) and `src/core/utils.ts`
+ * derives from it, so every ignore surface agrees instead of drifting (the
+ * pre-2026-07 state had four divergent copies). Add only UNAMBIGUOUS names —
+ * a project's own `.gitignore` / `.mnemonikignore` covers the ambiguous,
+ * project-specific cases (`vendor/`, custom dirs) hierarchically.
+ */
+export const BUILT_IN_IGNORE_DIRS = [
+    // JS / web
+    'node_modules',
+    '.next',
+    '.nuxt',
+    '.output',
+    'dist',
+    'build',
+    'coverage',
+    '.turbo',
+    '.vercel',
+    '.svelte-kit',
+    '.angular',
+    '.astro',
+    '.parcel-cache',
+    'bower_components',
+    // Python
+    'venv',
+    '.venv',
+    'env',
+    '__pycache__',
+    '.tox',
+    '.mypy_cache',
+    '.pytest_cache',
+    '.ruff_cache',
+    // Native mobile — iOS / Android / React Native / Flutter (2026-07-11 Pods incident)
+    'Pods',
+    'DerivedData',
+    '.gradle',
+    '.expo',
+    '.dart_tool',
+    // Infra / cloud
+    '.terraform',
+    'cdk.out',
+    '.serverless',
+    // Build systems, caches, VCS
+    'target',
+    'bin',
+    'obj',
+    '.cache',
+    '.git',
+    '.svn',
+    '.hg',
+];
+/**
+ * Non-directory built-in ignore patterns (files, globs, and the segment-
+ * anchored fixture rule), combined with BUILT_IN_IGNORE_DIRS to form
+ * DEFAULT_OPTIONS.ignorePatterns. See `shouldIgnore` for match semantics.
+ *
+ * `/tests/fixtures/*`: leading '/' = segment-anchored — matches tests/fixtures/
+ * at the path root or immediately after a '/', so nested packages/x/tests/
+ * fixtures/ are excluded but integration-tests/fixtures/ is NOT. Fixture
+ * snapshot dirs were being indexed as real source and outranking the genuine
+ * file in code_search. (Nested clones/worktrees/submodules are excluded
+ * generically by the isGitBoundary rule below, not a path convention.)
+ */
+const BUILT_IN_IGNORE_FILE_PATTERNS = [
+    '.env',
+    '.DS_Store',
+    '*.log',
+    '*.lock',
+    'package-lock.json',
+    'yarn.lock',
+    '*.min.js',
+    '*.min.css',
+    '*.bundle.js',
+    '*.legacy.js',
+    '*.map',
+    '/tests/fixtures/*',
+];
+/**
+ * Per-directory ignore files the walkers honor, unioned. `.gitignore` is the
+ * project's own declaration of generated/vendored paths; `.mnemonikignore`
+ * (same gitignore syntax) is the user's Mnemonik-specific "never index this"
+ * list (e.g. `secrets/`). Matched hierarchically via the `ignore` package.
+ */
+const IGNORE_FILE_NAMES = ['.gitignore', '.mnemonikignore'];
 const DEFAULT_OPTIONS = {
     maxChunkSize: 8000, // ~2000 tokens
     minChunkSize: 100,
-    ignorePatterns: [
-        // JavaScript/Node
-        'node_modules',
-        '.next',
-        // Python virtual environments
-        'venv',
-        '.venv',
-        'env',
-        '.env',
-        '__pycache__',
-        '.tox',
-        '.mypy_cache',
-        '.pytest_cache',
-        // Build outputs
-        'dist',
-        'build',
-        'target',
-        'bin',
-        'obj',
-        'coverage',
-        // Version control & cache
-        '.git',
-        '.cache',
-        '.DS_Store',
-        // Lock files
-        '*.log',
-        '*.lock',
-        'package-lock.json',
-        'yarn.lock',
-        // Minified/bundled files - too large and not useful for context
-        '*.min.js',
-        '*.min.css',
-        '*.bundle.js',
-        '*.legacy.js',
-        '*.map',
-        // Test fixture snapshot directories — historical before/after doc-truth
-        // dogfood copies (e.g. tests/fixtures/docTruth/*/before/src/...) were
-        // getting indexed as if they were real source, and a stale snapshot
-        // chunk could outrank the genuine file it duplicates in code_search
-        // (MemoryManager.searchCodePointers has a matching interim query-time
-        // exclusion for already-indexed rows; this is the scanner-level fix so
-        // new scans never pick them up in the first place). Retroactive cleanup
-        // of already-indexed fixture chunks happens on the next inventory diff —
-        // the daemon picks this up at its next package release, the in-process
-        // refresh tool gets it immediately.
-        //
-        // Leading '/' = segment-anchored (see shouldIgnore): matches tests/fixtures/
-        // at the path root or immediately after a '/' — so nested dirs like
-        // packages/x/tests/fixtures/ are also excluded, but integration-tests/fixtures/
-        // is NOT. The previous unanchored 'tests/fixtures/*' compiled to a bare
-        // substring regex and wrongly excluded any directory merely ENDING in "tests".
-        '/tests/fixtures/*',
-        // NOTE: transient agent worktrees (previously `.claude/worktrees/*`
-        // here) are no longer excluded by path convention. Linked worktrees,
-        // nested clones, and submodules are all excluded generically by the
-        // nested-git-boundary rule (isGitBoundary below) — git's own `.git`
-        // marker, so no host or codebase layout is baked in. Original incident:
-        // a worktree mirror was indexed as canonical source and polluted the
-        // corpus with 376 stale couplings.
-    ],
+    ignorePatterns: [...BUILT_IN_IGNORE_DIRS, ...BUILT_IN_IGNORE_FILE_PATTERNS],
     includeExtensions: [
         '.ts',
         '.tsx',
@@ -154,6 +183,90 @@ export class CodeScanner {
     constructor(options = {}) {
         this.options = { ...DEFAULT_OPTIONS, ...options };
     }
+    /**
+     * Read `.gitignore` + `.mnemonikignore` in `absDir` and compile them into one
+     * ignore layer (the two files are unioned — `.mnemonikignore` is just an
+     * additional gitignore-syntax exclusion list). Returns null when neither file
+     * exists. FAIL-CLOSED: a non-ENOENT read error (EISDIR, EACCES, timeout)
+     * latches `walk.complete = false` so callers deriving *removals* from the walk
+     * treat it as untrustworthy rather than silently ignoring nothing.
+     */
+    async loadIgnoreLayer(absDir, baseRel, walk) {
+        const patterns = [];
+        for (const name of IGNORE_FILE_NAMES) {
+            const filePath = join(absDir, name);
+            try {
+                const content = await withTimeout(readFile(filePath, 'utf-8'), FILE_OP_TIMEOUT_MS, `readFile timed out: ${filePath}`);
+                for (const line of content.split(/\r?\n/))
+                    patterns.push(line);
+            }
+            catch (err) {
+                if (err?.code !== 'ENOENT') {
+                    walk.complete = false;
+                    logDebug('Ignore-file read failed (fail-closed)', { path: filePath, err });
+                }
+            }
+        }
+        // `ignore` tolerates blank/comment lines; null when nothing meaningful.
+        if (patterns.length === 0)
+            return null;
+        const ig = ignore().add(patterns);
+        return { baseRel, ig };
+    }
+    /**
+     * True when `entryRel` (relative to the scan root) is excluded by any ignore
+     * layer in `stack`. Tested deepest-first: the first layer that explicitly
+     * ignores OR re-includes (via a `!negation`) wins, matching git's rule that a
+     * deeper `.gitignore` overrides a shallower one. Directories are tested with a
+     * trailing slash so `foo/` dir-only rules match the directory itself.
+     */
+    ignoredByStack(entryRel, isDir, stack) {
+        for (let i = stack.length - 1; i >= 0; i--) {
+            const { baseRel, ig } = stack[i];
+            let sub;
+            if (baseRel === '') {
+                sub = entryRel;
+            }
+            else if (entryRel === baseRel || !entryRel.startsWith(baseRel + '/')) {
+                continue; // this layer does not cover entryRel
+            }
+            else {
+                sub = entryRel.slice(baseRel.length + 1);
+            }
+            if (!sub)
+                continue;
+            const res = ig.test(isDir ? sub + '/' : sub);
+            if (res.ignored)
+                return true;
+            if (res.unignored)
+                return false;
+        }
+        return false;
+    }
+    /**
+     * Reconstruct the root→parent ignore-layer stack for a single file, for the
+     * incremental `scanFiles` path (which has a flat file list, not a recursive
+     * walk). Layers are memoized per directory in `cache` across a batch.
+     */
+    async buildIgnoreStackForFile(fileRel, rootPath, cache, walk) {
+        const dirs = [''];
+        let acc = '';
+        for (const seg of fileRel.split('/').slice(0, -1)) {
+            acc = acc === '' ? seg : `${acc}/${seg}`;
+            dirs.push(acc);
+        }
+        const stack = [];
+        for (const dir of dirs) {
+            let layer = cache.get(dir);
+            if (layer === undefined) {
+                layer = await this.loadIgnoreLayer(dir === '' ? rootPath : join(rootPath, dir), dir, walk);
+                cache.set(dir, layer);
+            }
+            if (layer)
+                stack.push(layer);
+        }
+        return stack;
+    }
     /**
      * True when any directory strictly between `rootPath` and `filePath`
      * carries its own `.git` entry (see isGitBoundary). Paths that don't
@@ -249,7 +362,7 @@ export class CodeScanner {
             complete: walk.complete,
         };
     }
-    async traversePaths(currentPath, rootPath, out, depth, walk) {
+    async traversePaths(currentPath, rootPath, out, depth, walk, stack = []) {
         if (depth >= CodeScanner.MAX_DEPTH)
             return;
         let entries;
@@ -261,6 +374,9 @@ export class CodeScanner {
             logDebug('Error traversing directory (listFiles)', { path: currentPath, error });
             return;
         }
+        const dirRel = currentPath === rootPath ? '' : relative(rootPath, currentPath).split(sep).join('/');
+        const localLayer = await this.loadIgnoreLayer(currentPath, dirRel, walk);
+        const localStack = localLayer ? [...stack, localLayer] : stack;
         for (const entry of entries) {
             const fullPath = join(currentPath, entry);
             const relativePath = relative(rootPath, fullPath);
@@ -278,11 +394,15 @@ export class CodeScanner {
                     ? await withTimeout(stat(fullPath), FILE_OP_TIMEOUT_MS, `stat timed out: ${fullPath}`)
                     : lstats;
                 if (stats.isDirectory()) {
+                    if (this.ignoredByStack(relativePath, true, localStack))
+                        continue; // .gitignore/.mnemonikignore
                     if (await isGitBoundary(fullPath))
                         continue; // another repo's subtree
-                    await this.traversePaths(fullPath, rootPath, out, depth + 1, walk);
+                    await this.traversePaths(fullPath, rootPath, out, depth + 1, walk, localStack);
                 }
                 else if (stats.isFile()) {
+                    if (this.ignoredByStack(relativePath, false, localStack))
+                        continue;
                     if (this.options.includeExtensions.includes(extname(fullPath))) {
                         out.push(relativePath);
                     }
@@ -300,11 +420,23 @@ export class CodeScanner {
      */
     async scanFiles(filePaths, rootPath) {
         const chunks = [];
+        const ignoreCache = new Map();
+        const walk = { complete: true };
         for (const filePath of filePaths) {
             try {
-                if (this.shouldIgnore(filePath)) {
+                const fileRel = rootPath ? relative(rootPath, filePath).split(sep).join('/') : filePath;
+                if (this.shouldIgnore(fileRel)) {
                     continue;
                 }
+                // Honor .gitignore/.mnemonikignore on the incremental path too, by
+                // reconstructing this file's ancestor ignore-layer stack (memoized
+                // per directory across the batch).
+                if (rootPath && !fileRel.startsWith('..')) {
+                    const stack = await this.buildIgnoreStackForFile(fileRel, rootPath, ignoreCache, walk);
+                    if (this.ignoredByStack(fileRel, false, stack)) {
+                        continue;
+                    }
+                }
                 // Explicit file lists arrive from watcher events, which can race a
                 // worktree/nested-clone appearing — apply the same nested-git-boundary
                 // rule the walks use (an ancestor between root and the file carrying
@@ -350,7 +482,7 @@ export class CodeScanner {
      * Recursively traverse directory
      * Added depth parameter with max limit
      */
-    async traverseDirectory(currentPath, rootPath, chunks, depth, walk) {
+    async traverseDirectory(currentPath, rootPath, chunks, depth, walk, stack = []) {
         // Prevent infinite recursion
         if (depth >= CodeScanner.MAX_DEPTH) {
             logDebug('Max directory depth reached, skipping', { path: currentPath, depth });
@@ -366,6 +498,10 @@ export class CodeScanner {
             logDebug('Error traversing directory', { path: currentPath, error });
             return;
         }
+        // Layer this directory's .gitignore/.mnemonikignore onto the inherited stack.
+        const dirRel = currentPath === rootPath ? '' : relative(rootPath, currentPath).split(sep).join('/');
+        const localLayer = await this.loadIgnoreLayer(currentPath, dirRel, walk);
+        const localStack = localLayer ? [...stack, localLayer] : stack;
         for (const entry of entries) {
             const fullPath = join(currentPath, entry);
             const relativePath = relative(rootPath, fullPath);
@@ -386,11 +522,15 @@ export class CodeScanner {
                     ? await withTimeout(stat(fullPath), FILE_OP_TIMEOUT_MS, `stat timed out: ${fullPath}`)
                     : lstats;
                 if (stats.isDirectory()) {
+                    if (this.ignoredByStack(relativePath, true, localStack))
+                        continue; // .gitignore/.mnemonikignore
                     if (await isGitBoundary(fullPath))
                         continue; // another repo's subtree
-                    await this.traverseDirectory(fullPath, rootPath, chunks, depth + 1, walk);
+                    await this.traverseDirectory(fullPath, rootPath, chunks, depth + 1, walk, localStack);
                 }
                 else if (stats.isFile()) {
+                    if (this.ignoredByStack(relativePath, false, localStack))
+                        continue;
                     const ext = extname(fullPath);
                     if (this.options.includeExtensions.includes(ext)) {
                         const fileChunks = await this.parseFile(fullPath, rootPath);
@@ -970,7 +1110,7 @@ export class CodeScanner {
         const out = [];
         const walkState = { complete: true };
         // M2: cap walk depth to match the scanner's MAX_DEPTH (10)
-        const walk = async (dir, depth) => {
+        const walk = async (dir, depth, stack = []) => {
             if (depth >= CodeScanner.MAX_DEPTH)
                 return;
             let entries;
@@ -981,6 +1121,9 @@ export class CodeScanner {
                 walkState.complete = false;
                 return;
             }
+            const dirRel = dir === projectRoot ? '' : relative(projectRoot, dir).split(sep).join('/');
+            const localLayer = await this.loadIgnoreLayer(dir, dirRel, walkState);
+            const localStack = localLayer ? [...stack, localLayer] : stack;
             for (const ent of entries) {
                 const full = join(dir, ent.name);
                 const rel = relative(projectRoot, full).split(sep).join('/');
@@ -1009,10 +1152,12 @@ export class CodeScanner {
                         continue;
                     }
                 }
+                if (this.ignoredByStack(rel, isDir, localStack))
+                    continue; // .gitignore/.mnemonikignore
                 if (isDir) {
                     if (await isGitBoundary(full))
                         continue; // another repo's subtree
-                    await walk(full, depth + 1);
+                    await walk(full, depth + 1, localStack);
                 }
                 else if (isFile && AUTHORITY_FILE_MATCHERS.some((m) => m(rel))) {
                     try {

package/dist/codeScanner.js.map

@@ -1 +1 @@
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package/dist/index.d.ts

@@ -6,7 +6,7 @@
  */
 export { MCP_INSTRUCTIONS, MCP_INSTRUCTIONS_RAW, getMcpInstructions } from './instructions.js';
 export { USAGE_GUIDE } from './usageGuide.js';
-export { CodeScanner, AUTHORITY_FILE_MATCHERS, isGitBoundary, FIXTURE_PATH_RE, isFixturePath, type CodeChunk, type ScanOptions, } from './codeScanner.js';
+export { CodeScanner, AUTHORITY_FILE_MATCHERS, BUILT_IN_IGNORE_DIRS, isGitBoundary, FIXTURE_PATH_RE, isFixturePath, type CodeChunk, type ScanOptions, } from './codeScanner.js';
 export { FileSystemReader, getFileSystemReader, type ScanFilesResult, type ChangedFilesResult, type FileData, } from './FileSystemReader.js';
 export { SECRET_PATTERNS, SECRET_REDACTION_PLACEHOLDER, scrubSecrets } from './secretPatterns.js';
 export { FETCH_TIMEOUT_MS, TELEMETRY_TIMEOUT_MS, POST_TOOL_TIMEOUT_MS, MCP_PRECHECK_TIMEOUT_MS, withHookTimeout, } from './hookTimeouts.js';

package/dist/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,oBAAoB,EAAE,kBAAkB,EAAE,MAAM,mBAAmB,CAAC;AAC/F,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAC;AAC9C,OAAO,EACL,WAAW,EACX,uBAAuB,EACvB,aAAa,EACb,eAAe,EACf,aAAa,EACb,KAAK,SAAS,EACd,KAAK,WAAW,GACjB,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EACL,gBAAgB,EAChB,mBAAmB,EACnB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,QAAQ,GACd,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,eAAe,EAAE,4BAA4B,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AAClG,OAAO,EACL,gBAAgB,EAChB,oBAAoB,EACpB,oBAAoB,EACpB,uBAAuB,EACvB,eAAe,GAChB,MAAM,mBAAmB,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,oBAAoB,EAAE,kBAAkB,EAAE,MAAM,mBAAmB,CAAC;AAC/F,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAC;AAC9C,OAAO,EACL,WAAW,EACX,uBAAuB,EACvB,oBAAoB,EACpB,aAAa,EACb,eAAe,EACf,aAAa,EACb,KAAK,SAAS,EACd,KAAK,WAAW,GACjB,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EACL,gBAAgB,EAChB,mBAAmB,EACnB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,QAAQ,GACd,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,eAAe,EAAE,4BAA4B,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AAClG,OAAO,EACL,gBAAgB,EAChB,oBAAoB,EACpB,oBAAoB,EACpB,uBAAuB,EACvB,eAAe,GAChB,MAAM,mBAAmB,CAAC"}

package/dist/index.js

@@ -6,7 +6,7 @@
  */
 export { MCP_INSTRUCTIONS, MCP_INSTRUCTIONS_RAW, getMcpInstructions } from './instructions.js';
 export { USAGE_GUIDE } from './usageGuide.js';
-export { CodeScanner, AUTHORITY_FILE_MATCHERS, isGitBoundary, FIXTURE_PATH_RE, isFixturePath, } from './codeScanner.js';
+export { CodeScanner, AUTHORITY_FILE_MATCHERS, BUILT_IN_IGNORE_DIRS, isGitBoundary, FIXTURE_PATH_RE, isFixturePath, } from './codeScanner.js';
 export { FileSystemReader, getFileSystemReader, } from './FileSystemReader.js';
 export { SECRET_PATTERNS, SECRET_REDACTION_PLACEHOLDER, scrubSecrets } from './secretPatterns.js';
 export { FETCH_TIMEOUT_MS, TELEMETRY_TIMEOUT_MS, POST_TOOL_TIMEOUT_MS, MCP_PRECHECK_TIMEOUT_MS, withHookTimeout, } from './hookTimeouts.js';

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,oBAAoB,EAAE,kBAAkB,EAAE,MAAM,mBAAmB,CAAC;AAC/F,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAC;AAC9C,OAAO,EACL,WAAW,EACX,uBAAuB,EACvB,aAAa,EACb,eAAe,EACf,aAAa,GAGd,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EACL,gBAAgB,EAChB,mBAAmB,GAIpB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,eAAe,EAAE,4BAA4B,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AAClG,OAAO,EACL,gBAAgB,EAChB,oBAAoB,EACpB,oBAAoB,EACpB,uBAAuB,EACvB,eAAe,GAChB,MAAM,mBAAmB,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,oBAAoB,EAAE,kBAAkB,EAAE,MAAM,mBAAmB,CAAC;AAC/F,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAC;AAC9C,OAAO,EACL,WAAW,EACX,uBAAuB,EACvB,oBAAoB,EACpB,aAAa,EACb,eAAe,EACf,aAAa,GAGd,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EACL,gBAAgB,EAChB,mBAAmB,GAIpB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,eAAe,EAAE,4BAA4B,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AAClG,OAAO,EACL,gBAAgB,EAChB,oBAAoB,EACpB,oBAAoB,EACpB,uBAAuB,EACvB,eAAe,GAChB,MAAM,mBAAmB,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mnemonik/shared",
-  "version": "6.2.8",
+  "version": "6.3.0",
   "description": "Shared constants and utilities for Mnemonik packages",
   "type": "module",
   "main": "dist/index.js",
@@ -23,6 +23,9 @@
   ],
   "author": "Anthony",
   "license": "MIT",
+  "dependencies": {
+    "ignore": "^7.0.5"
+  },
   "devDependencies": {
     "typescript": "^5.3.3"
   }

package/src/FileSystemReader.ts

@@ -17,6 +17,11 @@ import { CodeScanner, CodeChunk } from './codeScanner.js';
 const FILE_OP_TIMEOUT_MS = 5000;
 const MAX_FILE_SIZE = 10 * 1024 * 1024; // 10 MB
 
+// NOTE: this SKIP_DIRS is NOT an index gate — FileSystemReader's walk methods
+// (scanDirectory/detectChangedFiles) have no live caller; only readFileContent
+// (single file, no ignore) is used, for JIT citation verification. The
+// authoritative built-in list is BUILT_IN_IGNORE_DIRS in codeScanner.ts. Left
+// as-is (dead) rather than rewired to avoid churn on unused code.
 const SKIP_DIRS = new Set([
   'node_modules',
   '.git',

package/src/codeScanner.ts

@@ -5,6 +5,7 @@
 import { readdir, readFile, stat, lstat, realpath } from 'fs/promises';
 import { join, relative, extname, sep } from 'path';
 import { createHash } from 'crypto';
+import ignore, { type Ignore } from 'ignore';
 import { debug as logDebug } from './logger.js';
 import { withTimeout } from './asyncUtils.js';
 import { scrubSecrets } from './secretPatterns.js';
@@ -50,69 +51,100 @@ interface WalkState {
   complete: boolean;
 }
 
+/**
+ * Directory basenames the scanner never indexes, across every ecosystem —
+ * generated output, package-manager/build caches, and vendored deps. SINGLE
+ * SOURCE OF TRUTH: the scanner package's discovery + watch walks import this
+ * (`packages/scanner/src/{discovery,watcher}.ts`) and `src/core/utils.ts`
+ * derives from it, so every ignore surface agrees instead of drifting (the
+ * pre-2026-07 state had four divergent copies). Add only UNAMBIGUOUS names —
+ * a project's own `.gitignore` / `.mnemonikignore` covers the ambiguous,
+ * project-specific cases (`vendor/`, custom dirs) hierarchically.
+ */
+export const BUILT_IN_IGNORE_DIRS: readonly string[] = [
+  // JS / web
+  'node_modules',
+  '.next',
+  '.nuxt',
+  '.output',
+  'dist',
+  'build',
+  'coverage',
+  '.turbo',
+  '.vercel',
+  '.svelte-kit',
+  '.angular',
+  '.astro',
+  '.parcel-cache',
+  'bower_components',
+  // Python
+  'venv',
+  '.venv',
+  'env',
+  '__pycache__',
+  '.tox',
+  '.mypy_cache',
+  '.pytest_cache',
+  '.ruff_cache',
+  // Native mobile — iOS / Android / React Native / Flutter (2026-07-11 Pods incident)
+  'Pods',
+  'DerivedData',
+  '.gradle',
+  '.expo',
+  '.dart_tool',
+  // Infra / cloud
+  '.terraform',
+  'cdk.out',
+  '.serverless',
+  // Build systems, caches, VCS
+  'target',
+  'bin',
+  'obj',
+  '.cache',
+  '.git',
+  '.svn',
+  '.hg',
+];
+
+/**
+ * Non-directory built-in ignore patterns (files, globs, and the segment-
+ * anchored fixture rule), combined with BUILT_IN_IGNORE_DIRS to form
+ * DEFAULT_OPTIONS.ignorePatterns. See `shouldIgnore` for match semantics.
+ *
+ * `/tests/fixtures/*`: leading '/' = segment-anchored — matches tests/fixtures/
+ * at the path root or immediately after a '/', so nested packages/x/tests/
+ * fixtures/ are excluded but integration-tests/fixtures/ is NOT. Fixture
+ * snapshot dirs were being indexed as real source and outranking the genuine
+ * file in code_search. (Nested clones/worktrees/submodules are excluded
+ * generically by the isGitBoundary rule below, not a path convention.)
+ */
+const BUILT_IN_IGNORE_FILE_PATTERNS: readonly string[] = [
+  '.env',
+  '.DS_Store',
+  '*.log',
+  '*.lock',
+  'package-lock.json',
+  'yarn.lock',
+  '*.min.js',
+  '*.min.css',
+  '*.bundle.js',
+  '*.legacy.js',
+  '*.map',
+  '/tests/fixtures/*',
+];
+
+/**
+ * Per-directory ignore files the walkers honor, unioned. `.gitignore` is the
+ * project's own declaration of generated/vendored paths; `.mnemonikignore`
+ * (same gitignore syntax) is the user's Mnemonik-specific "never index this"
+ * list (e.g. `secrets/`). Matched hierarchically via the `ignore` package.
+ */
+const IGNORE_FILE_NAMES = ['.gitignore', '.mnemonikignore'] as const;
+
 const DEFAULT_OPTIONS: Required<ScanOptions> = {
   maxChunkSize: 8000, // ~2000 tokens
   minChunkSize: 100,
-  ignorePatterns: [
-    // JavaScript/Node
-    'node_modules',
-    '.next',
-    // Python virtual environments
-    'venv',
-    '.venv',
-    'env',
-    '.env',
-    '__pycache__',
-    '.tox',
-    '.mypy_cache',
-    '.pytest_cache',
-    // Build outputs
-    'dist',
-    'build',
-    'target',
-    'bin',
-    'obj',
-    'coverage',
-    // Version control & cache
-    '.git',
-    '.cache',
-    '.DS_Store',
-    // Lock files
-    '*.log',
-    '*.lock',
-    'package-lock.json',
-    'yarn.lock',
-    // Minified/bundled files - too large and not useful for context
-    '*.min.js',
-    '*.min.css',
-    '*.bundle.js',
-    '*.legacy.js',
-    '*.map',
-    // Test fixture snapshot directories — historical before/after doc-truth
-    // dogfood copies (e.g. tests/fixtures/docTruth/*/before/src/...) were
-    // getting indexed as if they were real source, and a stale snapshot
-    // chunk could outrank the genuine file it duplicates in code_search
-    // (MemoryManager.searchCodePointers has a matching interim query-time
-    // exclusion for already-indexed rows; this is the scanner-level fix so
-    // new scans never pick them up in the first place). Retroactive cleanup
-    // of already-indexed fixture chunks happens on the next inventory diff —
-    // the daemon picks this up at its next package release, the in-process
-    // refresh tool gets it immediately.
-    //
-    // Leading '/' = segment-anchored (see shouldIgnore): matches tests/fixtures/
-    // at the path root or immediately after a '/' — so nested dirs like
-    // packages/x/tests/fixtures/ are also excluded, but integration-tests/fixtures/
-    // is NOT. The previous unanchored 'tests/fixtures/*' compiled to a bare
-    // substring regex and wrongly excluded any directory merely ENDING in "tests".
-    '/tests/fixtures/*',
-    // NOTE: transient agent worktrees (previously `.claude/worktrees/*`
-    // here) are no longer excluded by path convention. Linked worktrees,
-    // nested clones, and submodules are all excluded generically by the
-    // nested-git-boundary rule (isGitBoundary below) — git's own `.git`
-    // marker, so no host or codebase layout is baked in. Original incident:
-    // a worktree mirror was indexed as canonical source and polluted the
-    // corpus with 376 stale couplings.
-  ],
+  ignorePatterns: [...BUILT_IN_IGNORE_DIRS, ...BUILT_IN_IGNORE_FILE_PATTERNS],
   includeExtensions: [
     '.ts',
     '.tsx',
@@ -195,6 +227,18 @@ export async function isGitBoundary(dirPath: string): Promise<boolean> {
   }
 }
 
+/**
+ * One directory's compiled ignore-file rules, keyed by its path relative to
+ * the scan root (`''` = root). A stack of these, root→leaf, is threaded
+ * through the walkers; `ignoredByStack` tests deepest-first so a nested
+ * `.gitignore` overrides a shallower one (git precedence).
+ */
+interface IgnoreLayer {
+  baseRel: string;
+  ig: Ignore;
+}
+type IgnoreStack = IgnoreLayer[];
+
 export class CodeScanner {
   private options: Required<ScanOptions>;
 
@@ -202,6 +246,97 @@ export class CodeScanner {
     this.options = { ...DEFAULT_OPTIONS, ...options };
   }
 
+  /**
+   * Read `.gitignore` + `.mnemonikignore` in `absDir` and compile them into one
+   * ignore layer (the two files are unioned — `.mnemonikignore` is just an
+   * additional gitignore-syntax exclusion list). Returns null when neither file
+   * exists. FAIL-CLOSED: a non-ENOENT read error (EISDIR, EACCES, timeout)
+   * latches `walk.complete = false` so callers deriving *removals* from the walk
+   * treat it as untrustworthy rather than silently ignoring nothing.
+   */
+  private async loadIgnoreLayer(
+    absDir: string,
+    baseRel: string,
+    walk: WalkState
+  ): Promise<IgnoreLayer | null> {
+    const patterns: string[] = [];
+    for (const name of IGNORE_FILE_NAMES) {
+      const filePath = join(absDir, name);
+      try {
+        const content = await withTimeout(
+          readFile(filePath, 'utf-8'),
+          FILE_OP_TIMEOUT_MS,
+          `readFile timed out: ${filePath}`
+        );
+        for (const line of content.split(/\r?\n/)) patterns.push(line);
+      } catch (err) {
+        if ((err as NodeJS.ErrnoException)?.code !== 'ENOENT') {
+          walk.complete = false;
+          logDebug('Ignore-file read failed (fail-closed)', { path: filePath, err });
+        }
+      }
+    }
+    // `ignore` tolerates blank/comment lines; null when nothing meaningful.
+    if (patterns.length === 0) return null;
+    const ig = ignore().add(patterns);
+    return { baseRel, ig };
+  }
+
+  /**
+   * True when `entryRel` (relative to the scan root) is excluded by any ignore
+   * layer in `stack`. Tested deepest-first: the first layer that explicitly
+   * ignores OR re-includes (via a `!negation`) wins, matching git's rule that a
+   * deeper `.gitignore` overrides a shallower one. Directories are tested with a
+   * trailing slash so `foo/` dir-only rules match the directory itself.
+   */
+  private ignoredByStack(entryRel: string, isDir: boolean, stack: IgnoreStack): boolean {
+    for (let i = stack.length - 1; i >= 0; i--) {
+      const { baseRel, ig } = stack[i];
+      let sub: string;
+      if (baseRel === '') {
+        sub = entryRel;
+      } else if (entryRel === baseRel || !entryRel.startsWith(baseRel + '/')) {
+        continue; // this layer does not cover entryRel
+      } else {
+        sub = entryRel.slice(baseRel.length + 1);
+      }
+      if (!sub) continue;
+      const res = ig.test(isDir ? sub + '/' : sub);
+      if (res.ignored) return true;
+      if (res.unignored) return false;
+    }
+    return false;
+  }
+
+  /**
+   * Reconstruct the root→parent ignore-layer stack for a single file, for the
+   * incremental `scanFiles` path (which has a flat file list, not a recursive
+   * walk). Layers are memoized per directory in `cache` across a batch.
+   */
+  private async buildIgnoreStackForFile(
+    fileRel: string,
+    rootPath: string,
+    cache: Map<string, IgnoreLayer | null>,
+    walk: WalkState
+  ): Promise<IgnoreStack> {
+    const dirs = [''];
+    let acc = '';
+    for (const seg of fileRel.split('/').slice(0, -1)) {
+      acc = acc === '' ? seg : `${acc}/${seg}`;
+      dirs.push(acc);
+    }
+    const stack: IgnoreStack = [];
+    for (const dir of dirs) {
+      let layer = cache.get(dir);
+      if (layer === undefined) {
+        layer = await this.loadIgnoreLayer(dir === '' ? rootPath : join(rootPath, dir), dir, walk);
+        cache.set(dir, layer);
+      }
+      if (layer) stack.push(layer);
+    }
+    return stack;
+  }
+
   /**
    * True when any directory strictly between `rootPath` and `filePath`
    * carries its own `.git` entry (see isGitBoundary). Paths that don't
@@ -309,7 +444,8 @@ export class CodeScanner {
     rootPath: string,
     out: string[],
     depth: number,
-    walk: WalkState
+    walk: WalkState,
+    stack: IgnoreStack = []
   ): Promise<void> {
     if (depth >= CodeScanner.MAX_DEPTH) return;
     let entries: string[];
@@ -324,6 +460,10 @@ export class CodeScanner {
       logDebug('Error traversing directory (listFiles)', { path: currentPath, error });
       return;
     }
+    const dirRel =
+      currentPath === rootPath ? '' : relative(rootPath, currentPath).split(sep).join('/');
+    const localLayer = await this.loadIgnoreLayer(currentPath, dirRel, walk);
+    const localStack = localLayer ? [...stack, localLayer] : stack;
     for (const entry of entries) {
       const fullPath = join(currentPath, entry);
       const relativePath = relative(rootPath, fullPath);
@@ -346,9 +486,11 @@ export class CodeScanner {
           : lstats;
 
         if (stats.isDirectory()) {
+          if (this.ignoredByStack(relativePath, true, localStack)) continue; // .gitignore/.mnemonikignore
           if (await isGitBoundary(fullPath)) continue; // another repo's subtree
-          await this.traversePaths(fullPath, rootPath, out, depth + 1, walk);
+          await this.traversePaths(fullPath, rootPath, out, depth + 1, walk, localStack);
         } else if (stats.isFile()) {
+          if (this.ignoredByStack(relativePath, false, localStack)) continue;
           if (this.options.includeExtensions.includes(extname(fullPath))) {
             out.push(relativePath);
           }
@@ -366,12 +508,24 @@ export class CodeScanner {
    */
   async scanFiles(filePaths: string[], rootPath: string): Promise<CodeChunk[]> {
     const chunks: CodeChunk[] = [];
+    const ignoreCache = new Map<string, IgnoreLayer | null>();
+    const walk: WalkState = { complete: true };
 
     for (const filePath of filePaths) {
       try {
-        if (this.shouldIgnore(filePath)) {
+        const fileRel = rootPath ? relative(rootPath, filePath).split(sep).join('/') : filePath;
+        if (this.shouldIgnore(fileRel)) {
           continue;
         }
+        // Honor .gitignore/.mnemonikignore on the incremental path too, by
+        // reconstructing this file's ancestor ignore-layer stack (memoized
+        // per directory across the batch).
+        if (rootPath && !fileRel.startsWith('..')) {
+          const stack = await this.buildIgnoreStackForFile(fileRel, rootPath, ignoreCache, walk);
+          if (this.ignoredByStack(fileRel, false, stack)) {
+            continue;
+          }
+        }
         // Explicit file lists arrive from watcher events, which can race a
         // worktree/nested-clone appearing — apply the same nested-git-boundary
         // rule the walks use (an ancestor between root and the file carrying
@@ -424,7 +578,8 @@ export class CodeScanner {
     rootPath: string,
     chunks: CodeChunk[],
     depth: number,
-    walk: WalkState
+    walk: WalkState,
+    stack: IgnoreStack = []
   ): Promise<void> {
     // Prevent infinite recursion
     if (depth >= CodeScanner.MAX_DEPTH) {
@@ -446,6 +601,12 @@ export class CodeScanner {
       return;
     }
 
+    // Layer this directory's .gitignore/.mnemonikignore onto the inherited stack.
+    const dirRel =
+      currentPath === rootPath ? '' : relative(rootPath, currentPath).split(sep).join('/');
+    const localLayer = await this.loadIgnoreLayer(currentPath, dirRel, walk);
+    const localStack = localLayer ? [...stack, localLayer] : stack;
+
     for (const entry of entries) {
       const fullPath = join(currentPath, entry);
       const relativePath = relative(rootPath, fullPath);
@@ -475,9 +636,11 @@ export class CodeScanner {
           : lstats;
 
         if (stats.isDirectory()) {
+          if (this.ignoredByStack(relativePath, true, localStack)) continue; // .gitignore/.mnemonikignore
           if (await isGitBoundary(fullPath)) continue; // another repo's subtree
-          await this.traverseDirectory(fullPath, rootPath, chunks, depth + 1, walk);
+          await this.traverseDirectory(fullPath, rootPath, chunks, depth + 1, walk, localStack);
         } else if (stats.isFile()) {
+          if (this.ignoredByStack(relativePath, false, localStack)) continue;
           const ext = extname(fullPath);
           if (this.options.includeExtensions.includes(ext)) {
             const fileChunks = await this.parseFile(fullPath, rootPath);
@@ -1123,7 +1286,7 @@ export class CodeScanner {
     const walkState: WalkState = { complete: true };
 
     // M2: cap walk depth to match the scanner's MAX_DEPTH (10)
-    const walk = async (dir: string, depth: number): Promise<void> => {
+    const walk = async (dir: string, depth: number, stack: IgnoreStack = []): Promise<void> => {
       if (depth >= CodeScanner.MAX_DEPTH) return;
       let entries;
       try {
@@ -1132,6 +1295,9 @@ export class CodeScanner {
         walkState.complete = false;
         return;
       }
+      const dirRel = dir === projectRoot ? '' : relative(projectRoot, dir).split(sep).join('/');
+      const localLayer = await this.loadIgnoreLayer(dir, dirRel, walkState);
+      const localStack = localLayer ? [...stack, localLayer] : stack;
       for (const ent of entries) {
         const full = join(dir, ent.name);
         const rel = relative(projectRoot, full).split(sep).join('/');
@@ -1159,9 +1325,10 @@ export class CodeScanner {
           }
         }
 
+        if (this.ignoredByStack(rel, isDir, localStack)) continue; // .gitignore/.mnemonikignore
         if (isDir) {
           if (await isGitBoundary(full)) continue; // another repo's subtree
-          await walk(full, depth + 1);
+          await walk(full, depth + 1, localStack);
         } else if (isFile && AUTHORITY_FILE_MATCHERS.some((m) => m(rel))) {
           try {
             let content = await readFile(full, 'utf-8');

package/src/index.ts

@@ -10,6 +10,7 @@ export { USAGE_GUIDE } from './usageGuide.js';
 export {
   CodeScanner,
   AUTHORITY_FILE_MATCHERS,
+  BUILT_IN_IGNORE_DIRS,
   isGitBoundary,
   FIXTURE_PATH_RE,
   isFixturePath,