agentmap 0.8.0 → 0.9.0

package/dist/map/truncate.js

@@ -1,11 +1,40 @@
-// Truncate definitions in map to limit context size.
+// Truncate definitions and descriptions in map to limit context size.
 const DEFAULT_MAX_DEFS = 25;
+const DEFAULT_MAX_DESC_CHARS = 300;
 /**
  * Check if a def value indicates exported or extern
  */
 function isExportedDef(value) {
     return value.includes('exported') || value.includes('extern');
 }
+/**
+ * Truncate description by character count, rounding up to include the full line
+ * that crosses the limit (in excess).
+ */
+function truncateDescriptionByChars(description, maxChars) {
+    if (description.length <= maxChars)
+        return description;
+    const lines = description.split('\n');
+    // Single-line fallback: hard-truncate at maxChars
+    if (lines.length === 1) {
+        return description.slice(0, maxChars) + '...';
+    }
+    let charCount = 0;
+    for (let i = 0; i < lines.length; i++) {
+        // +1 for the newline separator (except first line)
+        charCount += lines[i].length + (i > 0 ? 1 : 0);
+        if (charCount >= maxChars) {
+            // Include this line (in excess), then stop
+            const kept = lines.slice(0, i + 1);
+            const remaining = lines.length - kept.length;
+            if (remaining > 0) {
+                kept.push(`... and ${remaining} more lines`);
+            }
+            return kept.join('\n');
+        }
+    }
+    return description;
+}
 /**
  * Check if a value is a FileEntry (has description or defs)
  */
@@ -23,12 +52,53 @@ function isSubmoduleEntry(value) {
         return false;
     return 'submodule' in value;
 }
+/**
+ * Recursively truncate a submodule node while preserving its metadata keys.
+ */
+function truncateSubmoduleNode(entry, options) {
+    const result = { submodule: entry.submodule };
+    if (entry.dirty) {
+        result.dirty = entry.dirty;
+    }
+    for (const [key, value] of Object.entries(entry)) {
+        if (key === 'submodule' || key === 'dirty') {
+            continue;
+        }
+        if (isFileEntry(value)) {
+            result[key] = truncateFileEntry(value, options);
+        }
+        else if (isSubmoduleEntry(value)) {
+            result[key] = truncateSubmoduleNode(value, options);
+        }
+        else if (value && typeof value === 'object') {
+            result[key] = truncateMap(value, options);
+        }
+    }
+    return result;
+}
+/**
+ * Truncate a file entry: cap description by chars and defs by count.
+ */
+function truncateFileEntry(entry, options) {
+    let result = entry;
+    // Truncate description by character count
+    const maxDescChars = options.maxDescChars ?? DEFAULT_MAX_DESC_CHARS;
+    if (result.description && result.description.length > maxDescChars) {
+        result = { ...result, description: truncateDescriptionByChars(result.description, maxDescChars) };
+    }
+    // Truncate defs
+    result = truncateDefs(result, options.maxDefs);
+    return result;
+}
 /**
  * Truncate definitions in a file entry to maxDefs
  * If file has exported symbols, shows only exports field instead
  * Otherwise uses current truncation behavior
  */
-export function truncateDefs(entry, maxDefs = DEFAULT_MAX_DEFS) {
+export function truncateDefs(entry, maxDefsOrOptions) {
+    const maxDefs = typeof maxDefsOrOptions === 'number'
+        ? maxDefsOrOptions
+        : (maxDefsOrOptions?.maxDefs ?? DEFAULT_MAX_DEFS);
     if (!entry.defs)
         return entry;
     const defNames = Object.keys(entry.defs);
@@ -65,23 +135,22 @@ export function truncateDefs(entry, maxDefs = DEFAULT_MAX_DEFS) {
     return { ...entry, defs: truncated };
 }
 /**
- * Recursively truncate defs in all files in the map
+ * Recursively truncate defs and descriptions in all files in the map
  */
-export function truncateMap(node, maxDefs = DEFAULT_MAX_DEFS) {
+export function truncateMap(node, maxDefsOrOptions) {
+    const options = typeof maxDefsOrOptions === 'number'
+        ? { maxDefs: maxDefsOrOptions }
+        : (maxDefsOrOptions ?? {});
     const result = {};
     for (const [key, value] of Object.entries(node)) {
         if (isFileEntry(value)) {
-            result[key] = truncateDefs(value, maxDefs);
+            result[key] = truncateFileEntry(value, options);
         }
         else if (isSubmoduleEntry(value)) {
-            // Submodule entries pass through unchanged (no defs to truncate)
-            result[key] = value;
+            result[key] = truncateSubmoduleNode(value, options);
         }
         else if (value && typeof value === 'object') {
-            result[key] = truncateMap(value, maxDefs);
-        }
-        else {
-            result[key] = value;
+            result[key] = truncateMap(value, options);
         }
     }
     return result;

package/dist/map/truncate.js.map

@@ -1 +1 @@
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+{"version":3,"file":"truncate.js","sourceRoot":"","sources":["../../src/map/truncate.ts"],"names":[],"mappings":"AAAA,sEAAsE;AAItE,MAAM,gBAAgB,GAAG,EAAE,CAAA;AAC3B,MAAM,sBAAsB,GAAG,GAAG,CAAA;AAOlC;;GAEG;AACH,SAAS,aAAa,CAAC,KAAa;IAClC,OAAO,KAAK,CAAC,QAAQ,CAAC,UAAU,CAAC,IAAI,KAAK,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAA;AAC/D,CAAC;AAED;;;GAGG;AACH,SAAS,0BAA0B,CAAC,WAAmB,EAAE,QAAgB;IACvE,IAAI,WAAW,CAAC,MAAM,IAAI,QAAQ;QAAE,OAAO,WAAW,CAAA;IAEtD,MAAM,KAAK,GAAG,WAAW,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAErC,kDAAkD;IAClD,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACvB,OAAO,WAAW,CAAC,KAAK,CAAC,CAAC,EAAE,QAAQ,CAAC,GAAG,KAAK,CAAA;IAC/C,CAAC;IAED,IAAI,SAAS,GAAG,CAAC,CAAA;IAEjB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACtC,mDAAmD;QACnD,SAAS,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAC9C,IAAI,SAAS,IAAI,QAAQ,EAAE,CAAC;YAC1B,2CAA2C;YAC3C,MAAM,IAAI,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAA;YAClC,MAAM,SAAS,GAAG,KAAK,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;YAC5C,IAAI,SAAS,GAAG,CAAC,EAAE,CAAC;gBAClB,IAAI,CAAC,IAAI,CAAC,WAAW,SAAS,aAAa,CAAC,CAAA;YAC9C,CAAC;YACD,OAAO,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACxB,CAAC;IACH,CAAC;IAED,OAAO,WAAW,CAAA;AACpB,CAAC;AAED;;GAEG;AACH,SAAS,WAAW,CAAC,KAAc;IACjC,IAAI,CAAC,KAAK,IAAI,OAAO,KAAK,KAAK,QAAQ;QAAE,OAAO,KAAK,CAAA;IACrD,MAAM,GAAG,GAAG,KAAgC,CAAA;IAC5C,OAAO,aAAa,IAAI,GAAG,IAAI,MAAM,IAAI,GAAG,CAAA;AAC9C,CAAC;AAED;;GAEG;AACH,SAAS,gBAAgB,CAAC,KAAc;IACtC,IAAI,CAAC,KAAK,IAAI,OAAO,KAAK,KAAK,QAAQ;QAAE,OAAO,KAAK,CAAA;IACrD,OAAO,WAAW,IAAK,KAAiC,CAAA;AAC1D,CAAC;AAED;;GAEG;AACH,SAAS,qBAAqB,CAAC,KAAoB,EAAE,OAAwB;IAC3E,MAAM,MAAM,GAAkB,EAAE,SAAS,EAAE,KAAK,CAAC,SAAS,EAAE,CAAA;IAE5D,IAAI,KAAK,CAAC,KAAK,EAAE,CAAC;QAChB,MAAM,CAAC,KAAK,GAAG,KAAK,CAAC,KAAK,CAAA;IAC5B,CAAC;IAED,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC;QACjD,IAAI,GAAG,KAAK,WAAW,IAAI,GAAG,KAAK,OAAO,EAAE,CAAC;YAC3C,SAAQ;QACV,CAAC;QAED,IAAI,WAAW,CAAC,KAAK,CAAC,EAAE,CAAC;YACvB,MAAM,CAAC,GAAG,CAAC,GAAG,iBAAiB,CAAC,KAAK,EAAE,OAAO,CAAC,CAAA;QACjD,CAAC;aAAM,IAAI,gBAAgB,CAAC,KAAK,CAAC,EAAE,CAAC;YACnC,MAAM,CAAC,GAAG,CAAC,GAAG,qBAAqB,CAAC,KAAsB,EAAE,OAAO,CAAC,CAAA;QACtE,CAAC;aAAM,IAAI,KAAK,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE,CAAC;YAC9C,MAAM,CAAC,GAAG,CAAC,GAAG,WAAW,CAAC,KAAgB,EAAE,OAAO,CAAC,CAAA;QACtD,CAAC;IACH,CAAC;IAED,OAAO,MAAM,CAAA;AACf,CAAC;AAED;;GAEG;AACH,SAAS,iBAAiB,CAAC,KAAgB,EAAE,OAAwB;IACnE,IAAI,MAAM,GAAG,KAAK,CAAA;IAElB,0CAA0C;IAC1C,MAAM,YAAY,GAAG,OAAO,CAAC,YAAY,IAAI,sBAAsB,CAAA;IACnE,IAAI,MAAM,CAAC,WAAW,IAAI,MAAM,CAAC,WAAW,CAAC,MAAM,GAAG,YAAY,EAAE,CAAC;QACnE,MAAM,GAAG,EAAE,GAAG,MAAM,EAAE,WAAW,EAAE,0BAA0B,CAAC,MAAM,CAAC,WAAW,EAAE,YAAY,CAAC,EAAE,CAAA;IACnG,CAAC;IAED,gBAAgB;IAChB,MAAM,GAAG,YAAY,CAAC,MAAM,EAAE,OAAO,CAAC,OAAO,CAAC,CAAA;IAC9C,OAAO,MAAM,CAAA;AACf,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,YAAY,CAAC,KAAgB,EAAE,gBAA2C;IACxF,MAAM,OAAO,GAAG,OAAO,gBAAgB,KAAK,QAAQ;QAClD,CAAC,CAAC,gBAAgB;QAClB,CAAC,CAAC,CAAC,gBAAgB,EAAE,OAAO,IAAI,gBAAgB,CAAC,CAAA;IAEnD,IAAI,CAAC,KAAK,CAAC,IAAI;QAAE,OAAO,KAAK,CAAA;IAE7B,MAAM,QAAQ,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IACxC,IAAI,QAAQ,CAAC,MAAM,IAAI,OAAO;QAAE,OAAO,KAAK,CAAA;IAE5C,6CAA6C;IAC7C,MAAM,aAAa,GAAG,QAAQ,CAAC,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,aAAa,CAAC,KAAK,CAAC,IAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAE/E,wDAAwD;IACxD,IAAI,aAAa,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC7B,MAAM,OAAO,GAAa,EAAE,CAAA;QAC5B,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,aAAa,CAAC,MAAM,EAAE,OAAO,CAAC,CAAA;QAE1D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;YACpC,MAAM,IAAI,GAAG,aAAa,CAAC,CAAC,CAAC,CAAA;YAC7B,OAAO,CAAC,IAAI,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClC,CAAC;QAED,4CAA4C;QAC5C,IAAI,aAAa,CAAC,MAAM,GAAG,OAAO,EAAE,CAAC;YACnC,MAAM,SAAS,GAAG,aAAa,CAAC,MAAM,GAAG,OAAO,CAAA;YAChD,OAAO,CAAC,UAAU,SAAS,IAAI,CAAC,GAAG,GAAG,SAAS,eAAe,CAAA;QAChE,CAAC;QAED,sCAAsC;QACtC,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,EAAE,GAAG,KAAK,CAAA;QAC/B,OAAO,EAAE,GAAG,IAAI,EAAE,OAAO,EAAE,CAAA;IAC7B,CAAC;IAED,qDAAqD;IACrD,MAAM,SAAS,GAAa,EAAE,CAAA;IAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,EAAE,CAAC,EAAE,EAAE,CAAC;QACjC,MAAM,IAAI,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;QACxB,SAAS,CAAC,IAAI,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IACpC,CAAC;IAED,MAAM,SAAS,GAAG,QAAQ,CAAC,MAAM,GAAG,OAAO,CAAA;IAC3C,+CAA+C;IAC/C,SAAS,CAAC,UAAU,SAAS,IAAI,CAAC,GAAG,GAAG,SAAS,mBAAmB,CAAA;IAEpE,OAAO,EAAE,GAAG,KAAK,EAAE,IAAI,EAAE,SAAS,EAAE,CAAA;AACtC,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,WAAW,CAAC,IAAa,EAAE,gBAA2C;IACpF,MAAM,OAAO,GAAoB,OAAO,gBAAgB,KAAK,QAAQ;QACnE,CAAC,CAAC,EAAE,OAAO,EAAE,gBAAgB,EAAE;QAC/B,CAAC,CAAC,CAAC,gBAAgB,IAAI,EAAE,CAAC,CAAA;IAE5B,MAAM,MAAM,GAAY,EAAE,CAAA;IAE1B,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;QAChD,IAAI,WAAW,CAAC,KAAK,CAAC,EAAE,CAAC;YACvB,MAAM,CAAC,GAAG,CAAC,GAAG,iBAAiB,CAAC,KAAK,EAAE,OAAO,CAAC,CAAA;QACjD,CAAC;aAAM,IAAI,gBAAgB,CAAC,KAAK,CAAC,EAAE,CAAC;YACnC,MAAM,CAAC,GAAG,CAAC,GAAG,qBAAqB,CAAC,KAAsB,EAAE,OAAO,CAAC,CAAA;QACtE,CAAC;aAAM,IAAI,KAAK,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE,CAAC;YAC9C,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package/dist/scanner.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"scanner.d.ts","sourceRoot":"","sources":["../src/scanner.ts"],"names":[],"mappings":"AAYA,OAAO,KAAK,EAAE,UAAU,EAAE,eAAe,EAA2B,aAAa,EAAE,MAAM,YAAY,CAAA;AAuDrG;;GAEG;AACH,MAAM,WAAW,UAAU;IACzB,KAAK,EAAE,UAAU,EAAE,CAAA;IACnB,UAAU,EAAE,aAAa,EAAE,CAAA;CAC5B;AAED;;GAEG;AACH,wBAAsB,aAAa,CAAC,OAAO,GAAE,eAAoB,GAAG,OAAO,CAAC,UAAU,CAAC,CA+FtF"}
+{"version":3,"file":"scanner.d.ts","sourceRoot":"","sources":["../src/scanner.ts"],"names":[],"mappings":"AAcA,OAAO,KAAK,EAAE,UAAU,EAAE,eAAe,EAA2B,aAAa,EAAE,MAAM,YAAY,CAAA;AAsHrG;;GAEG;AACH,MAAM,WAAW,UAAU;IACzB,KAAK,EAAE,UAAU,EAAE,CAAA;IACnB,UAAU,EAAE,aAAa,EAAE,CAAA;CAC5B;AAuJD;;GAEG;AACH,wBAAsB,aAAa,CAAC,OAAO,GAAE,eAAoB,GAAG,OAAO,CAAC,UAAU,CAAC,CAetF"}

package/dist/scanner.js

@@ -1,5 +1,6 @@
-// Scan directory for files with header comments/docstrings.
+// Scan directory for files with header comments/docstrings and recurse into submodules.
 import { execSync } from 'child_process';
+import { realpathSync } from 'fs';
 import pLimit from 'p-limit';
 import picomatch from 'picomatch';
 import { readFile } from 'fs/promises';
@@ -8,6 +9,7 @@ import { extractMarkerFromCode, extractMarkdownDescription } from './extract/mar
 import { extractDefinitions } from './extract/definitions.js';
 import { getAllDiffData, applyDiffToDefinitions } from './extract/git-status.js';
 import { getSubmodules, getSubmodulePaths } from './extract/submodules.js';
+import { createConsoleLogger } from './logger.js';
 import { parseCode, detectLanguage, LANGUAGE_EXTENSIONS } from './parser/index.js';
 /**
  * Maximum number of files to process (safety limit)
@@ -33,116 +35,213 @@ function isReadmeFile(filepath) {
     return filename === 'readme.md' || filename === 'readme';
 }
 /**
- * Get tracked files using git ls-files
- * Only returns files that are tracked by git (committed or staged)
+ * Get tracked files using git ls-files -z -s.
+ * NUL-delimited for safe cross-platform parsing of any filename.
+ * Filters out symlinks (mode 120000).
+ * Returns path + blob SHA for duplicate detection.
+ *
+ * Format per entry: "<mode> <sha> <stage>\t<path>\0"
  */
 function getGitFiles(dir) {
     const maxBuffer = 1024 * 10000000;
     try {
-        // Get only tracked files
-        const stdout = execSync('git ls-files', {
+        const stdout = execSync('git ls-files -z -s', {
             cwd: dir,
             maxBuffer,
             encoding: 'utf8',
         });
-        return stdout
-            .split(/\r?\n/)
-            .map(x => x.trim())
-            .filter(Boolean)
-            .map(normalize);
+        const results = [];
+        // Split on NUL byte, filter empty trailing entry
+        const entries = stdout.split('\0').filter(Boolean);
+        for (const entry of entries) {
+            // Format: "<mode> <sha> <stage>\t<path>"
+            const tabIdx = entry.indexOf('\t');
+            if (tabIdx === -1)
+                continue;
+            const meta = entry.slice(0, tabIdx);
+            const path = entry.slice(tabIdx + 1);
+            const spaceIdx = meta.indexOf(' ');
+            if (spaceIdx === -1)
+                continue;
+            const mode = meta.slice(0, spaceIdx);
+            const sha = meta.slice(spaceIdx + 1, meta.indexOf(' ', spaceIdx + 1));
+            // Skip symlinks (mode 120000)
+            if (mode === '120000')
+                continue;
+            results.push({ path: normalize(path), sha });
+        }
+        return results;
     }
     catch {
         return [];
     }
 }
 /**
- * Scan directory and process files with header comments
+ * Build a map of blob SHA → shortest path for duplicate detection.
+ * Files sharing the same blob SHA are exact duplicates in git.
  */
-export async function scanDirectory(options = {}) {
-    const dir = options.dir ?? process.cwd();
-    // Filter out null/undefined/empty patterns (cac can pass [null] when option not used)
-    const ignorePatterns = (options.ignore ?? []).filter((p) => !!p);
-    const filterPatterns = (options.filter ?? []).filter((p) => !!p);
-    const includeDiff = options.diff ?? false;
-    const includeSubmodules = options.submodules !== false; // default true
-    // Detect submodules first (needed for both map entries and diff filtering)
-    let submodules = [];
-    let submodulePathSet = new Set();
-    if (includeSubmodules) {
-        submodules = getSubmodules(dir);
-        submodulePathSet = new Set(submodules.map(s => s.path));
+function buildDuplicateMap(files, pathPrefix) {
+    // Group paths by SHA
+    const shaToEntries = new Map();
+    for (const { path, sha } of files) {
+        const prefixed = joinRelativePath(pathPrefix, path);
+        const existing = shaToEntries.get(sha);
+        if (existing) {
+            existing.push(prefixed);
+        }
+        else {
+            shaToEntries.set(sha, [prefixed]);
+        }
+    }
+    // For each group with >1 file, shortest path is the original
+    const duplicateOf = new Map();
+    for (const paths of shaToEntries.values()) {
+        if (paths.length < 2)
+            continue;
+        paths.sort((a, b) => a.length - b.length || a.localeCompare(b));
+        const original = paths[0];
+        for (let i = 1; i < paths.length; i++) {
+            duplicateOf.set(paths[i], original);
+        }
+    }
+    return duplicateOf;
+}
+function normalizeRelativePath(path) {
+    return path.replace(/\\/g, '/');
+}
+function joinRelativePath(prefix, path) {
+    const normalizedPath = normalizeRelativePath(path);
+    return prefix ? `${prefix}/${normalizedPath}` : normalizedPath;
+}
+function getCanonicalRepoDir(dir) {
+    try {
+        return realpathSync(dir);
+    }
+    catch {
+        return dir;
     }
-    else {
-        // Even when not showing submodules, detect paths for diff filtering
-        submodulePathSet = getSubmodulePaths(dir);
+}
+async function scanRepo(options) {
+    const canonicalRepoDir = getCanonicalRepoDir(options.repoDir);
+    if (options.visitedRepoDirs.has(canonicalRepoDir)) {
+        return { files: [], submodules: [] };
+    }
+    options.visitedRepoDirs.add(canonicalRepoDir);
+    let submodules = [];
+    const directSubmodules = options.includeSubmodules ? getSubmodules(options.repoDir) : [];
+    const directSubmodulePathSet = options.includeSubmodules
+        ? new Set(directSubmodules.map(submodule => submodule.path))
+        : getSubmodulePaths(options.repoDir);
+    if (options.includeSubmodules) {
+        submodules = directSubmodules.map(submodule => ({
+            ...submodule,
+            path: joinRelativePath(options.pathPrefix, submodule.path),
+        }));
     }
-    // Build a normalized set for filtering (handles Windows backslash paths)
     const normalizedSubmodulePaths = new Set();
-    for (const p of submodulePathSet) {
-        normalizedSubmodulePaths.add(normalize(p));
-    }
-    // Get file list from git (caller should ensure we're in a git repo)
-    let files = getGitFiles(dir);
-    // Filter out submodule gitlink entries (they appear as paths in ls-files)
-    // Use normalized paths to handle Windows backslash vs forward slash differences
-    files = files.filter(f => !normalizedSubmodulePaths.has(f));
-    // Filter by supported extensions or README files
-    files = files.filter(f => isSupportedFile(f) || isReadmeFile(f));
-    // Filter by filter patterns (only include matching files)
-    if (filterPatterns.length > 0) {
-        const isIncluded = picomatch(filterPatterns);
-        files = files.filter(f => isIncluded(f));
-    }
-    // Filter by ignore patterns
-    if (ignorePatterns.length > 0) {
-        const isIgnored = picomatch(ignorePatterns);
-        files = files.filter(f => !isIgnored(f));
-    }
-    // Safety check: bail if too many files to avoid scanning huge directories
-    if (files.length > MAX_FILES) {
-        console.error(`Warning: Too many files (${files.length} > ${MAX_FILES}), skipping scan`);
+    for (const path of directSubmodulePathSet) {
+        normalizedSubmodulePaths.add(normalize(path));
+    }
+    const allGitFiles = getGitFiles(options.repoDir);
+    // Build duplicate map before filtering (needs all files to detect dupes)
+    const duplicateOf = buildDuplicateMap(allGitFiles, options.pathPrefix);
+    let gitFiles = allGitFiles.filter(f => !normalizedSubmodulePaths.has(f.path));
+    gitFiles = gitFiles.filter(f => isSupportedFile(f.path) || isReadmeFile(f.path));
+    gitFiles = gitFiles.filter(f => {
+        const relativePath = joinRelativePath(options.pathPrefix, f.path);
+        if (options.isIncluded && !options.isIncluded(relativePath)) {
+            return false;
+        }
+        if (options.isIgnored && options.isIgnored(relativePath)) {
+            return false;
+        }
+        return true;
+    });
+    if (gitFiles.length > MAX_FILES) {
+        options.logger?.warn(`Warning: Too many files (${gitFiles.length} > ${MAX_FILES}), skipping scan`);
         return { files: [], submodules };
     }
-    // Get git diff data if needed (isolated from main processing)
     let fileStats = null;
     let fileDiffs = null;
-    if (includeDiff) {
+    if (options.includeDiff) {
         try {
-            const diffData = getAllDiffData(dir, submodulePathSet);
+            const diffData = getAllDiffData(options.repoDir, directSubmodulePathSet, options.logger);
             fileStats = diffData.fileStats;
             fileDiffs = diffData.fileDiffs;
         }
         catch {
-            // Diff failed - continue without diff info
             fileStats = null;
             fileDiffs = null;
         }
     }
-    // Process files in parallel with concurrency limit
     const limit = pLimit(20);
-    const resultPromises = files.map(relativePath => {
-        const fullPath = join(dir, relativePath);
-        // Normalize path for lookup (handle Windows backslashes)
-        const normalizedPath = relativePath.replace(/\\/g, '/');
+    const resultPromises = gitFiles.map(({ path: relativePath }) => {
+        const fullPath = join(options.repoDir, relativePath);
+        const normalizedPath = normalizeRelativePath(relativePath);
+        const prefixedRelativePath = joinRelativePath(options.pathPrefix, relativePath);
         const fileDiff = fileDiffs?.get(normalizedPath);
         const stats = fileStats?.get(normalizedPath);
+        const dupOriginal = duplicateOf.get(prefixedRelativePath);
         return limit(async () => {
             try {
-                return await processFile(fullPath, relativePath, fileDiff, stats);
+                // If this file is a duplicate, return a stub pointing to the original
+                if (dupOriginal) {
+                    return {
+                        relativePath: prefixedRelativePath,
+                        duplicateOf: dupOriginal,
+                        definitions: [],
+                    };
+                }
+                return await processFile(fullPath, prefixedRelativePath, fileDiff, stats);
             }
-            catch (err) {
-                // Skip files that fail to process
-                console.error(`Warning: Failed to process ${relativePath}:`, err);
+            catch {
                 return null;
             }
         });
     });
+    const nestedResults = options.includeSubmodules
+        ? await Promise.all(directSubmodules.map(async (submodule) => {
+            if (!submodule.initialized) {
+                return { files: [], submodules: [] };
+            }
+            return scanRepo({
+                ...options,
+                repoDir: join(options.repoDir, submodule.path),
+                pathPrefix: joinRelativePath(options.pathPrefix, submodule.path),
+            });
+        }))
+        : [];
     const results = await Promise.all(resultPromises);
+    for (const nested of nestedResults) {
+        submodules.push(...nested.submodules);
+    }
     return {
-        files: results.filter((r) => r !== null),
+        files: [
+            ...results.filter((result) => result !== null),
+            ...nestedResults.flatMap(result => result.files),
+        ],
         submodules,
     };
 }
+/**
+ * Scan directory and process files with header comments
+ */
+export async function scanDirectory(options = {}) {
+    const dir = options.dir ?? process.cwd();
+    const logger = options.logger ?? createConsoleLogger();
+    const ignorePatterns = (options.ignore ?? []).filter((p) => !!p);
+    const filterPatterns = (options.filter ?? []).filter((p) => !!p);
+    return scanRepo({
+        repoDir: dir,
+        pathPrefix: '',
+        includeDiff: options.diff ?? false,
+        includeSubmodules: options.submodules !== false,
+        logger,
+        isIncluded: filterPatterns.length > 0 ? picomatch(filterPatterns) : undefined,
+        isIgnored: ignorePatterns.length > 0 ? picomatch(ignorePatterns) : undefined,
+        visitedRepoDirs: new Set(),
+    });
+}
 /**
  * Process a single file - check for marker and extract definitions
  */

package/dist/scanner.js.map

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package/dist/scanner.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=scanner.test.d.ts.map

package/dist/scanner.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"scanner.test.d.ts","sourceRoot":"","sources":["../src/scanner.test.ts"],"names":[],"mappings":""}

package/dist/scanner.test.js

@@ -0,0 +1,84 @@
+// Tests for recursive scanning across initialized git submodules.
+import { describe, expect, test } from 'bun:test';
+import { scanDirectory } from './scanner.js';
+import { addSubmodule, commitAll, createRepo, deinitSubmodule, updateSubmodulesRecursive, writeTrackedFile } from './test-helpers/git-test-helpers.js';
+describe('scanDirectory submodule recursion', () => {
+    test('includes files from initialized nested submodules under prefixed paths', async () => {
+        const nestedRepo = createRepo('agentmap-submodule-nested-');
+        writeTrackedFile(nestedRepo, 'README.md', '# Nested repo\n\nNested submodule README.');
+        commitAll(nestedRepo, 'Add nested repo README');
+        const childRepo = createRepo('agentmap-submodule-child-');
+        writeTrackedFile(childRepo, 'README.md', '# Child repo\n\nChild submodule README.');
+        commitAll(childRepo, 'Add child repo README');
+        addSubmodule(childRepo, nestedRepo.dir, 'deps/nested-lib');
+        commitAll(childRepo, 'Add nested submodule');
+        const rootRepo = createRepo('agentmap-submodule-root-');
+        writeTrackedFile(rootRepo, 'README.md', '# Root repo\n\nRoot repo README.');
+        commitAll(rootRepo, 'Add root README');
+        addSubmodule(rootRepo, childRepo.dir, 'vendor/child-lib');
+        commitAll(rootRepo, 'Add child submodule');
+        updateSubmodulesRecursive(rootRepo);
+        const result = await scanDirectory({ dir: rootRepo.dir });
+        expect(result.files.map(file => file.relativePath).sort()).toMatchInlineSnapshot(`
+[
+  "README.md",
+  "vendor/child-lib/README.md",
+  "vendor/child-lib/deps/nested-lib/README.md",
+]
+`);
+        expect(result.submodules.map(submodule => ({
+            path: submodule.path,
+            initialized: submodule.initialized,
+            dirty: submodule.dirty,
+            commitLength: submodule.commit.length,
+        }))).toMatchInlineSnapshot(`
+[
+  {
+    "commitLength": 7,
+    "dirty": false,
+    "initialized": true,
+    "path": "vendor/child-lib",
+  },
+  {
+    "commitLength": 7,
+    "dirty": false,
+    "initialized": true,
+    "path": "vendor/child-lib/deps/nested-lib",
+  },
+]
+`);
+    });
+    test('keeps uninitialized submodules as metadata-only nodes', async () => {
+        const childRepo = createRepo('agentmap-submodule-uninit-child-');
+        writeTrackedFile(childRepo, 'README.md', '# Child repo\n\nChild submodule README.');
+        commitAll(childRepo, 'Add child repo README');
+        const rootRepo = createRepo('agentmap-submodule-uninit-root-');
+        writeTrackedFile(rootRepo, 'README.md', '# Root repo\n\nRoot repo README.');
+        commitAll(rootRepo, 'Add root README');
+        addSubmodule(rootRepo, childRepo.dir, 'vendor/child-lib');
+        commitAll(rootRepo, 'Add child submodule');
+        deinitSubmodule(rootRepo, 'vendor/child-lib');
+        const result = await scanDirectory({ dir: rootRepo.dir });
+        expect(result.files.map(file => file.relativePath).sort()).toMatchInlineSnapshot(`
+[
+  "README.md",
+]
+`);
+        expect(result.submodules.map(submodule => ({
+            path: submodule.path,
+            initialized: submodule.initialized,
+            dirty: submodule.dirty,
+            commitLength: submodule.commit.length,
+        }))).toMatchInlineSnapshot(`
+[
+  {
+    "commitLength": 7,
+    "dirty": false,
+    "initialized": false,
+    "path": "vendor/child-lib",
+  },
+]
+`);
+    });
+});
+//# sourceMappingURL=scanner.test.js.map

package/dist/scanner.test.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"scanner.test.js","sourceRoot":"","sources":["../src/scanner.test.ts"],"names":[],"mappings":"AAAA,kEAAkE;AAElE,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,UAAU,CAAA;AACjD,OAAO,EAAE,aAAa,EAAE,MAAM,cAAc,CAAA;AAC5C,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,UAAU,EAAE,eAAe,EAAE,yBAAyB,EAAE,gBAAgB,EAAE,MAAM,oCAAoC,CAAA;AAEtJ,QAAQ,CAAC,mCAAmC,EAAE,GAAG,EAAE;IACjD,IAAI,CAAC,wEAAwE,EAAE,KAAK,IAAI,EAAE;QACxF,MAAM,UAAU,GAAG,UAAU,CAAC,4BAA4B,CAAC,CAAA;QAC3D,gBAAgB,CAAC,UAAU,EAAE,WAAW,EAAE,2CAA2C,CAAC,CAAA;QACtF,SAAS,CAAC,UAAU,EAAE,wBAAwB,CAAC,CAAA;QAE/C,MAAM,SAAS,GAAG,UAAU,CAAC,2BAA2B,CAAC,CAAA;QACzD,gBAAgB,CAAC,SAAS,EAAE,WAAW,EAAE,yCAAyC,CAAC,CAAA;QACnF,SAAS,CAAC,SAAS,EAAE,uBAAuB,CAAC,CAAA;QAC7C,YAAY,CAAC,SAAS,EAAE,UAAU,CAAC,GAAG,EAAE,iBAAiB,CAAC,CAAA;QAC1D,SAAS,CAAC,SAAS,EAAE,sBAAsB,CAAC,CAAA;QAE5C,MAAM,QAAQ,GAAG,UAAU,CAAC,0BAA0B,CAAC,CAAA;QACvD,gBAAgB,CAAC,QAAQ,EAAE,WAAW,EAAE,kCAAkC,CAAC,CAAA;QAC3E,SAAS,CAAC,QAAQ,EAAE,iBAAiB,CAAC,CAAA;QACtC,YAAY,CAAC,QAAQ,EAAE,SAAS,CAAC,GAAG,EAAE,kBAAkB,CAAC,CAAA;QACzD,SAAS,CAAC,QAAQ,EAAE,qBAAqB,CAAC,CAAA;QAC1C,yBAAyB,CAAC,QAAQ,CAAC,CAAA;QAEnC,MAAM,MAAM,GAAG,MAAM,aAAa,CAAC,EAAE,GAAG,EAAE,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAA;QAEzD,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,qBAAqB,CAAC;;;;;;CAMpF,CAAC,CAAA;QAEE,MAAM,CAAC,MAAM,CAAC,UAAU,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC,CAAC;YACzC,IAAI,EAAE,SAAS,CAAC,IAAI;YACpB,WAAW,EAAE,SAAS,CAAC,WAAW;YAClC,KAAK,EAAE,SAAS,CAAC,KAAK;YACtB,YAAY,EAAE,SAAS,CAAC,MAAM,CAAC,MAAM;SACtC,CAAC,CAAC,CAAC,CAAC,qBAAqB,CAAC;;;;;;;;;;;;;;;CAe9B,CAAC,CAAA;IACA,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,uDAAuD,EAAE,KAAK,IAAI,EAAE;QACvE,MAAM,SAAS,GAAG,UAAU,CAAC,kCAAkC,CAAC,CAAA;QAChE,gBAAgB,CAAC,SAAS,EAAE,WAAW,EAAE,yCAAyC,CAAC,CAAA;QACnF,SAAS,CAAC,SAAS,EAAE,uBAAuB,CAAC,CAAA;QAE7C,MAAM,QAAQ,GAAG,UAAU,CAAC,iCAAiC,CAAC,CAAA;QAC9D,gBAAgB,CAAC,QAAQ,EAAE,WAAW,EAAE,kCAAkC,CAAC,CAAA;QAC3E,SAAS,CAAC,QAAQ,EAAE,iBAAiB,CAAC,CAAA;QACtC,YAAY,CAAC,QAAQ,EAAE,SAAS,CAAC,GAAG,EAAE,kBAAkB,CAAC,CAAA;QACzD,SAAS,CAAC,QAAQ,EAAE,qBAAqB,CAAC,CAAA;QAC1C,eAAe,CAAC,QAAQ,EAAE,kBAAkB,CAAC,CAAA;QAE7C,MAAM,MAAM,GAAG,MAAM,aAAa,CAAC,EAAE,GAAG,EAAE,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAA;QAEzD,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,qBAAqB,CAAC;;;;CAIpF,CAAC,CAAA;QAEE,MAAM,CAAC,MAAM,CAAC,UAAU,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC,CAAC;YACzC,IAAI,EAAE,SAAS,CAAC,IAAI;YACpB,WAAW,EAAE,SAAS,CAAC,WAAW;YAClC,KAAK,EAAE,SAAS,CAAC,KAAK;YACtB,YAAY,EAAE,SAAS,CAAC,MAAM,CAAC,MAAM;SACtC,CAAC,CAAC,CAAC,CAAC,qBAAqB,CAAC;;;;;;;;;CAS9B,CAAC,CAAA;IACA,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}

package/dist/test-helpers/git-test-helpers.d.ts

@@ -0,0 +1,13 @@
+export interface TempRepo {
+    dir: string;
+}
+export declare function createTempDir(prefix: string): string;
+export declare function initRepo(dir: string): TempRepo;
+export declare function createRepo(prefix: string): TempRepo;
+export declare function writeTrackedFile(repo: TempRepo, relativePath: string, content: string): void;
+export declare function commitAll(repo: TempRepo, message: string): void;
+export declare function shortHead(repo: TempRepo): string;
+export declare function addSubmodule(repo: TempRepo, sourceDir: string, targetPath: string): void;
+export declare function updateSubmodulesRecursive(repo: TempRepo): void;
+export declare function deinitSubmodule(repo: TempRepo, targetPath: string): void;
+//# sourceMappingURL=git-test-helpers.d.ts.map

package/dist/test-helpers/git-test-helpers.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"git-test-helpers.d.ts","sourceRoot":"","sources":["../../src/test-helpers/git-test-helpers.ts"],"names":[],"mappings":"AAOA,MAAM,WAAW,QAAQ;IACvB,GAAG,EAAE,MAAM,CAAA;CACZ;AAUD,wBAAgB,aAAa,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAEpD;AAED,wBAAgB,QAAQ,CAAC,GAAG,EAAE,MAAM,GAAG,QAAQ,CAK9C;AAED,wBAAgB,UAAU,CAAC,MAAM,EAAE,MAAM,GAAG,QAAQ,CAInD;AAED,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,QAAQ,EAAE,YAAY,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,IAAI,CAI5F;AAED,wBAAgB,SAAS,CAAC,IAAI,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,GAAG,IAAI,CAG/D;AAED,wBAAgB,SAAS,CAAC,IAAI,EAAE,QAAQ,GAAG,MAAM,CAEhD;AAED,wBAAgB,YAAY,CAAC,IAAI,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,GAAG,IAAI,CAExF;AAED,wBAAgB,yBAAyB,CAAC,IAAI,EAAE,QAAQ,GAAG,IAAI,CAE9D;AAED,wBAAgB,eAAe,CAAC,IAAI,EAAE,QAAQ,EAAE,UAAU,EAAE,MAAM,GAAG,IAAI,CAExE"}