@sudosandwich/limps 2.13.1 → 2.13.3

package/dist/indexer.js.map

@@ -1 +1 @@
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package/dist/server-main.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"server-main.d.ts","sourceRoot":"","sources":["../src/server-main.ts"],"names":[],"mappings":"AAAA;;;GAGG;AA2BH;;;;GAIG;AACH,wBAAsB,cAAc,CAAC,aAAa,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CA4F1E"}
+{"version":3,"file":"server-main.d.ts","sourceRoot":"","sources":["../src/server-main.ts"],"names":[],"mappings":"AAAA;;;GAGG;AA8BH;;;;GAIG;AACH,wBAAsB,cAAc,CAAC,aAAa,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CA4I1E"}

package/dist/server-main.js

@@ -2,13 +2,14 @@
  * MCP Server startup logic.
  * Extracted from index.ts for use by CLI commands.
  */
-import { loadConfig, getAllDocsPaths, getFileExtensions, DEFAULT_DEBOUNCE_DELAY, } from './config.js';
+import { loadConfig, getAllDocsPaths, getFileExtensions, getMaxFileSize, getMaxDepth, DEFAULT_DEBOUNCE_DELAY, } from './config.js';
 import { createServer, startServer } from './server.js';
 import { resolve } from 'path';
 import { existsSync, mkdirSync } from 'fs';
 import { initializeDatabase, createSchema, indexAllPaths, indexDocument, removeDocument, } from './indexer.js';
 import { startWatcher, stopWatcher, DEFAULT_SETTLE_DELAY } from './watcher.js';
 import { resolveConfigPath } from './utils/config-resolver.js';
+import { checkFdBudget } from './utils/fd-safety.js';
 // Global references for graceful shutdown
 let watcher = null;
 let db = null;
@@ -18,6 +19,26 @@ let db = null;
  * @param configPathArg - Optional config path from CLI argument
  */
 export async function startMcpServer(configPathArg) {
+    // Close any previously opened resources to prevent FD leaks if called twice
+    // Best-effort cleanup: log failures but don't abort startup
+    if (watcher) {
+        try {
+            await stopWatcher(watcher);
+        }
+        catch (error) {
+            console.error('Failed to stop previous watcher during cleanup:', error);
+        }
+        watcher = null;
+    }
+    if (db) {
+        try {
+            db.close();
+        }
+        catch (error) {
+            console.error('Failed to close previous database during cleanup:', error);
+        }
+        db = null;
+    }
     // Resolve config path
     const configPath = resolveConfigPath(configPathArg);
     // Load configuration
@@ -32,7 +53,9 @@ export async function startMcpServer(configPathArg) {
     // Get all paths and extensions to index
     const docsPaths = getAllDocsPaths(config);
     const fileExtensions = getFileExtensions(config);
-    const ignorePatterns = ['.git', 'node_modules', '.tmp', '.obsidian'];
+    const maxFileSize = getMaxFileSize(config);
+    const maxDepth = getMaxDepth(config);
+    const ignorePatterns = ['.git', 'node_modules', '.tmp', '.obsidian', 'dist', 'build', '.cache'];
     // Validate paths before indexing — filter to only existing directories
     const validPaths = docsPaths.filter((p) => existsSync(p));
     if (!existsSync(config.plansPath)) {
@@ -48,7 +71,7 @@ export async function startMcpServer(configPathArg) {
     }
     // Initial indexing (only valid paths)
     if (validPaths.length > 0) {
-        const result = await indexAllPaths(db, validPaths, fileExtensions, ignorePatterns);
+        const result = await indexAllPaths(db, validPaths, fileExtensions, ignorePatterns, maxDepth, maxFileSize);
         console.error(`Indexed ${result.indexed} documents (${result.updated} updated, ${result.skipped} skipped)`);
         console.error(`Paths: ${validPaths.join(', ')}`);
         console.error(`Extensions: ${fileExtensions.join(', ')}`);
@@ -62,20 +85,33 @@ export async function startMcpServer(configPathArg) {
     else {
         console.error('No valid paths to index.');
     }
+    // Check FD budget before starting watcher
+    if (validPaths.length > 0) {
+        const budget = checkFdBudget(validPaths, maxDepth, ignorePatterns);
+        if (!budget.safe) {
+            console.error(`[limps] Warning: estimated ${budget.estimated} watch entries ` +
+                `but FD limit is ${budget.limit}. Consider reducing watch scope or running: ulimit -n 4096`);
+        }
+    }
     // Capture db reference for watcher callback
     const dbRef = db;
     // Start file watcher (only watch valid paths)
-    watcher = startWatcher(validPaths, async (path, event) => {
-        if (event === 'unlink') {
-            await removeDocument(dbRef, path);
-            console.error(`Removed document: ${path}`);
-        }
-        else {
-            await indexDocument(dbRef, path);
-            console.error(`Indexed document: ${path} (${event})`);
-        }
-    }, fileExtensions, ignorePatterns, DEFAULT_DEBOUNCE_DELAY, DEFAULT_SETTLE_DELAY);
-    console.error(`File watcher started for ${validPaths.length} path(s)`);
+    try {
+        watcher = await startWatcher(validPaths, async (path, event) => {
+            if (event === 'unlink') {
+                await removeDocument(dbRef, path);
+                console.error(`Removed document: ${path}`);
+            }
+            else {
+                await indexDocument(dbRef, path, maxFileSize);
+                console.error(`Indexed document: ${path} (${event})`);
+            }
+        }, fileExtensions, ignorePatterns, DEFAULT_DEBOUNCE_DELAY, DEFAULT_SETTLE_DELAY, undefined, maxDepth);
+        console.error(`File watcher started for ${validPaths.length} path(s)`);
+    }
+    catch (watchErr) {
+        console.error(`[limps] Warning: File watcher failed to start. The server will continue without live file watching.`, watchErr);
+    }
     // Create and start server
     const server = await createServer(config, db);
     await startServer(server, async () => {

package/dist/server-main.js.map

@@ -1 +1 @@
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+{"version":3,"file":"server-main.js","sourceRoot":"","sources":["../src/server-main.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EACL,UAAU,EACV,eAAe,EACf,iBAAiB,EACjB,cAAc,EACd,WAAW,EACX,sBAAsB,GACvB,MAAM,aAAa,CAAC;AACrB,OAAO,EAAE,YAAY,EAAE,WAAW,EAAE,MAAM,aAAa,CAAC;AACxD,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAC;AAC/B,OAAO,EAAE,UAAU,EAAE,SAAS,EAAE,MAAM,IAAI,CAAC;AAG3C,OAAO,EACL,kBAAkB,EAClB,YAAY,EACZ,aAAa,EACb,aAAa,EACb,cAAc,GACf,MAAM,cAAc,CAAC;AACtB,OAAO,EAAE,YAAY,EAAE,WAAW,EAAE,oBAAoB,EAAE,MAAM,cAAc,CAAC;AAC/E,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAC;AAErD,0CAA0C;AAC1C,IAAI,OAAO,GAAwB,IAAI,CAAC;AACxC,IAAI,EAAE,GAAwB,IAAI,CAAC;AAEnC;;;;GAIG;AACH,MAAM,CAAC,KAAK,UAAU,cAAc,CAAC,aAAsB;IACzD,4EAA4E;IAC5E,4DAA4D;IAC5D,IAAI,OAAO,EAAE,CAAC;QACZ,IAAI,CAAC;YACH,MAAM,WAAW,CAAC,OAAO,CAAC,CAAC;QAC7B,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,OAAO,CAAC,KAAK,CAAC,iDAAiD,EAAE,KAAK,CAAC,CAAC;QAC1E,CAAC;QACD,OAAO,GAAG,IAAI,CAAC;IACjB,CAAC;IACD,IAAI,EAAE,EAAE,CAAC;QACP,IAAI,CAAC;YACH,EAAE,CAAC,KAAK,EAAE,CAAC;QACb,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,OAAO,CAAC,KAAK,CAAC,mDAAmD,EAAE,KAAK,CAAC,CAAC;QAC5E,CAAC;QACD,EAAE,GAAG,IAAI,CAAC;IACZ,CAAC;IAED,sBAAsB;IACtB,MAAM,UAAU,GAAG,iBAAiB,CAAC,aAAa,CAAC,CAAC;IAEpD,qBAAqB;IACrB,MAAM,MAAM,GAAG,UAAU,CAAC,UAAU,CAAC,CAAC;IAEtC,+BAA+B;IAC/B,SAAS,CAAC,MAAM,CAAC,QAAQ,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IAEhD,sBAAsB;IACtB,MAAM,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,QAAQ,EAAE,kBAAkB,CAAC,CAAC;IAC5D,EAAE,GAAG,kBAAkB,CAAC,MAAM,CAAC,CAAC;IAChC,YAAY,CAAC,EAAE,CAAC,CAAC;IACjB,OAAO,CAAC,KAAK,CAAC,2BAA2B,MAAM,EAAE,CAAC,CAAC;IAEnD,wCAAwC;IACxC,MAAM,SAAS,GAAG,eAAe,CAAC,MAAM,CAAC,CAAC;IAC1C,MAAM,cAAc,GAAG,iBAAiB,CAAC,MAAM,CAAC,CAAC;IACjD,MAAM,WAAW,GAAG,cAAc,CAAC,MAAM,CAAC,CAAC;IAC3C,MAAM,QAAQ,GAAG,WAAW,CAAC,MAAM,CAAC,CAAC;IACrC,MAAM,cAAc,GAAG,CAAC,MAAM,EAAE,cAAc,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,EAAE,OAAO,EAAE,QAAQ,CAAC,CAAC;IAEhG,uEAAuE;IACvE,MAAM,UAAU,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC;IAC1D,IAAI,CAAC,UAAU,CAAC,MAAM,CAAC,SAAS,CAAC,EAAE,CAAC;QAClC,OAAO,CAAC,KAAK,CACX,oCAAoC;YAClC,MAAM,CAAC,SAAS;YAChB,sCAAsC,CACzC,CAAC;QACF,OAAO,CAAC,KAAK,CAAC,0EAA0E,CAAC,CAAC;IAC5F,CAAC;IACD,KAAK,MAAM,CAAC,IAAI,SAAS,EAAE,CAAC;QAC1B,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,MAAM,CAAC,SAAS,EAAE,CAAC;YAC7C,OAAO,CAAC,KAAK,CAAC,2CAA2C,CAAC,aAAa,CAAC,CAAC;QAC3E,CAAC;IACH,CAAC;IAED,sCAAsC;IACtC,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC1B,MAAM,MAAM,GAAG,MAAM,aAAa,CAChC,EAAE,EACF,UAAU,EACV,cAAc,EACd,cAAc,EACd,QAAQ,EACR,WAAW,CACZ,CAAC;QACF,OAAO,CAAC,KAAK,CACX,WAAW,MAAM,CAAC,OAAO,eAAe,MAAM,CAAC,OAAO,aAAa,MAAM,CAAC,OAAO,WAAW,CAC7F,CAAC;QACF,OAAO,CAAC,KAAK,CAAC,UAAU,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACjD,OAAO,CAAC,KAAK,CAAC,eAAe,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC1D,IAAI,MAAM,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC7B,OAAO,CAAC,KAAK,CAAC,oBAAoB,MAAM,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC;YAC1D,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,MAAM,EAAE,CAAC;gBAChC,OAAO,CAAC,KAAK,CAAC,OAAO,GAAG,CAAC,IAAI,KAAK,GAAG,CAAC,KAAK,EAAE,CAAC,CAAC;YACjD,CAAC;QACH,CAAC;IACH,CAAC;SAAM,CAAC;QACN,OAAO,CAAC,KAAK,CAAC,0BAA0B,CAAC,CAAC;IAC5C,CAAC;IAED,0CAA0C;IAC1C,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC1B,MAAM,MAAM,GAAG,aAAa,CAAC,UAAU,EAAE,QAAQ,EAAE,cAAc,CAAC,CAAC;QACnE,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,CAAC;YACjB,OAAO,CAAC,KAAK,CACX,8BAA8B,MAAM,CAAC,SAAS,iBAAiB;gBAC7D,mBAAmB,MAAM,CAAC,KAAK,4DAA4D,CAC9F,CAAC;QACJ,CAAC;IACH,CAAC;IAED,4CAA4C;IAC5C,MAAM,KAAK,GAAG,EAAE,CAAC;IAEjB,8CAA8C;IAC9C,IAAI,CAAC;QACH,OAAO,GAAG,MAAM,YAAY,CAC1B,UAAU,EACV,KAAK,EAAE,IAAI,EAAE,KAAK,EAAE,EAAE;YACpB,IAAI,KAAK,KAAK,QAAQ,EAAE,CAAC;gBACvB,MAAM,cAAc,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC;gBAClC,OAAO,CAAC,KAAK,CAAC,qBAAqB,IAAI,EAAE,CAAC,CAAC;YAC7C,CAAC;iBAAM,CAAC;gBACN,MAAM,aAAa,CAAC,KAAK,EAAE,IAAI,EAAE,WAAW,CAAC,CAAC;gBAC9C,OAAO,CAAC,KAAK,CAAC,qBAAqB,IAAI,KAAK,KAAK,GAAG,CAAC,CAAC;YACxD,CAAC;QACH,CAAC,EACD,cAAc,EACd,cAAc,EACd,sBAAsB,EACtB,oBAAoB,EACpB,SAAS,EACT,QAAQ,CACT,CAAC;QACF,OAAO,CAAC,KAAK,CAAC,4BAA4B,UAAU,CAAC,MAAM,UAAU,CAAC,CAAC;IACzE,CAAC;IAAC,OAAO,QAAQ,EAAE,CAAC;QAClB,OAAO,CAAC,KAAK,CACX,qGAAqG,EACrG,QAAQ,CACT,CAAC;IACJ,CAAC;IAED,0BAA0B;IAC1B,MAAM,MAAM,GAAG,MAAM,YAAY,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;IAC9C,MAAM,WAAW,CAAC,MAAM,EAAE,KAAK,IAAI,EAAE;QACnC,6BAA6B;QAC7B,IAAI,OAAO,EAAE,CAAC;YACZ,MAAM,WAAW,CAAC,OAAO,CAAC,CAAC;YAC3B,OAAO,CAAC,KAAK,CAAC,sBAAsB,CAAC,CAAC;YACtC,OAAO,GAAG,IAAI,CAAC;QACjB,CAAC;QACD,IAAI,EAAE,EAAE,CAAC;YACP,EAAE,CAAC,KAAK,EAAE,CAAC;YACX,OAAO,CAAC,KAAK,CAAC,4BAA4B,CAAC,CAAC;YAC5C,EAAE,GAAG,IAAI,CAAC;QACZ,CAAC;IACH,CAAC,CAAC,CAAC;AACL,CAAC"}

package/dist/server.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"server.d.ts","sourceRoot":"","sources":["../src/server.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAEpE,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAChD,OAAO,KAAK,EAAE,QAAQ,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAC;AAI/D,OAAO,EAKL,KAAK,eAAe,EACrB,MAAM,wBAAwB,CAAC;AAEhC;;;;;;;GAOG;AACH,wBAAsB,YAAY,CAChC,MAAM,EAAE,YAAY,EACpB,EAAE,EAAE,YAAY,GACf,OAAO,CAAC,SAAS,GAAG;IAAE,gBAAgB,CAAC,EAAE,eAAe,EAAE,CAAA;CAAE,CAAC,CAgE/D;AAED;;;;;GAKG;AACH,wBAAsB,WAAW,CAC/B,MAAM,EAAE,SAAS,EACjB,UAAU,CAAC,EAAE,MAAM,OAAO,CAAC,IAAI,CAAC,GAC/B,OAAO,CAAC,IAAI,CAAC,CA0Ef"}
+{"version":3,"file":"server.d.ts","sourceRoot":"","sources":["../src/server.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAEpE,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAChD,OAAO,KAAK,EAAE,QAAQ,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAC;AAI/D,OAAO,EAKL,KAAK,eAAe,EACrB,MAAM,wBAAwB,CAAC;AAEhC;;;;;;;GAOG;AACH,wBAAsB,YAAY,CAChC,MAAM,EAAE,YAAY,EACpB,EAAE,EAAE,YAAY,GACf,OAAO,CAAC,SAAS,GAAG;IAAE,gBAAgB,CAAC,EAAE,eAAe,EAAE,CAAA;CAAE,CAAC,CAgE/D;AAED;;;;;GAKG;AACH,wBAAsB,WAAW,CAC/B,MAAM,EAAE,SAAS,EACjB,UAAU,CAAC,EAAE,MAAM,OAAO,CAAC,IAAI,CAAC,GAC/B,OAAO,CAAC,IAAI,CAAC,CAiFf"}

package/dist/server.js

@@ -73,7 +73,13 @@ export async function startServer(server, onShutdown) {
     // Set up signal handlers for graceful shutdown
     // Only register exit handlers if not in test environment
     const isTestEnvironment = process.env.NODE_ENV === 'test' || process.env.VITEST === 'true';
+    let shuttingDown = false;
     const shutdown = async (signal) => {
+        if (shuttingDown) {
+            console.error(`Received ${signal} during shutdown, ignoring.`);
+            return;
+        }
+        shuttingDown = true;
         console.error(`Received ${signal}, shutting down gracefully...`);
         try {
             // Shutdown extensions first

package/dist/server.js.map

@@ -1 +1 @@
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package/dist/tools/create-doc.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"create-doc.d.ts","sourceRoot":"","sources":["../../src/tools/create-doc.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAGxB,OAAO,EAAgC,KAAK,OAAO,EAAE,MAAM,mBAAmB,CAAC;AAG/E,OAAO,KAAK,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,aAAa,CAAC;AAE3D;;GAEG;AACH,eAAO,MAAM,oBAAoB;;;;;;;;;;iBAW/B,CAAC;AAEH,MAAM,MAAM,cAAc,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAElE;;GAEG;AACH,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,IAAI,CAAC;IACd,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,OAAO,CAAC;CACf;AAED;;;GAGG;AACH,eAAO,MAAM,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAqB5C,CAAC;AAmBF;;;;;;;GAOG;AACH,wBAAsB,eAAe,CACnC,KAAK,EAAE,cAAc,EACrB,OAAO,EAAE,WAAW,GACnB,OAAO,CAAC,UAAU,CAAC,CA4FrB"}
+{"version":3,"file":"create-doc.d.ts","sourceRoot":"","sources":["../../src/tools/create-doc.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAGxB,OAAO,EAAgC,KAAK,OAAO,EAAE,MAAM,mBAAmB,CAAC;AAY/E,OAAO,KAAK,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,aAAa,CAAC;AAE3D;;GAEG;AACH,eAAO,MAAM,oBAAoB;;;;;;;;;;iBAW/B,CAAC;AAEH,MAAM,MAAM,cAAc,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAElE;;GAEG;AACH,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,IAAI,CAAC;IACd,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,OAAO,CAAC;CACf;AAED;;;GAGG;AACH,eAAO,MAAM,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAqB5C,CAAC;AAWF;;;;;;;GAOG;AACH,wBAAsB,eAAe,CACnC,KAAK,EAAE,cAAc,EACrB,OAAO,EAAE,WAAW,GACnB,OAAO,CAAC,UAAU,CAAC,CAkHrB"}

package/dist/tools/create-doc.js

@@ -5,8 +5,11 @@ import { z } from 'zod';
 import { existsSync, writeFileSync, mkdirSync, statSync } from 'fs';
 import { dirname } from 'path';
 import { validatePath, isWritablePath } from '../utils/paths.js';
-import { alreadyExists, restrictedPath, permissionDenied, noSpaceError } from '../utils/errors.js';
+import { alreadyExists, restrictedPath, permissionDenied, noSpaceError, validationError, } from '../utils/errors.js';
 import { indexDocument } from '../indexer.js';
+import { getMaxFileSize } from '../config.js';
+import { getDocsRoot } from '../utils/repo-root.js';
+import { checkSymlinkAncestors, checkPathContainment } from '../utils/fs-safety.js';
 /**
  * Input schema for create_doc tool.
  */
@@ -48,13 +51,6 @@ type: "research"
     example: '',
     none: '',
 };
-/**
- * Get repository root from config.
- * Assumes plansPath is ../plans relative to .mcp, so dirname gives repo root.
- */
-function getRepoRoot(config) {
-    return dirname(config.plansPath);
-}
 /**
  * Apply template to content, replacing {{DATE}} with current date.
  */
@@ -73,7 +69,7 @@ function applyTemplate(template, content) {
  */
 export async function handleCreateDoc(input, context) {
     const { path, content, template, prettyPrint = false } = input;
-    const repoRoot = getRepoRoot(context.config);
+    const repoRoot = getDocsRoot(context.config);
     try {
         // Validate path (must not exist, must be writable)
         const validated = validatePath(path, repoRoot, {
@@ -92,11 +88,22 @@ export async function handleCreateDoc(input, context) {
         if (template !== 'none' && TEMPLATES[template]) {
             finalContent = applyTemplate(TEMPLATES[template], content);
         }
+        // Reject content exceeding maximum file size
+        const maxFileSize = getMaxFileSize(context.config);
+        if (Buffer.byteLength(finalContent, 'utf-8') > maxFileSize) {
+            throw validationError('content', `Content size exceeds maximum allowed file size (${maxFileSize} bytes)`);
+        }
         // Create parent directories if needed
         const parentDir = dirname(validated.absolute);
         if (!existsSync(parentDir)) {
             mkdirSync(parentDir, { recursive: true });
         }
+        // Security: Check for symlink traversal before writing
+        // This prevents writes via symlinked parent directories
+        const ancestorCheck = checkSymlinkAncestors(validated.absolute, repoRoot);
+        if (!ancestorCheck.safe) {
+            throw permissionDenied(validated.relative, ancestorCheck.reason, 'write');
+        }
         // Write file with error handling
         try {
             writeFileSync(validated.absolute, finalContent, 'utf-8');
@@ -112,11 +119,16 @@ export async function handleCreateDoc(input, context) {
             }
             throw error;
         }
+        // After write, verify the resolved path is still within repo root
+        const containmentCheck = checkPathContainment(validated.absolute, repoRoot);
+        if (!containmentCheck.safe) {
+            throw permissionDenied(validated.relative, containmentCheck.reason, 'write');
+        }
         // Get file size
         const stats = statSync(validated.absolute);
         const size = stats.size;
-        // Index the new file
-        await indexDocument(context.db, validated.absolute);
+        // Index the new file, passing maxFileSize to ensure consistent validation
+        await indexDocument(context.db, validated.absolute, maxFileSize);
         const output = {
             path: validated.relative,
             created: true,

package/dist/tools/create-doc.js.map

@@ -1 +1 @@
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package/dist/tools/delete-doc.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"delete-doc.d.ts","sourceRoot":"","sources":["../../src/tools/delete-doc.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAGxB,OAAO,KAAK,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,aAAa,CAAC;AAO3D;;GAEG;AACH,eAAO,MAAM,SAAS,WAAW,CAAC;AAElC;;GAEG;AACH,eAAO,MAAM,eAAe,EAAE,SAAS,MAAM,EAO5C,CAAC;AAEF;;GAEG;AACH,eAAO,MAAM,oBAAoB;;;;iBAI/B,CAAC;AAEH,MAAM,MAAM,cAAc,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAElE;;GAEG;AACH,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AA4BD;;;;;;;GAOG;AACH,wBAAsB,eAAe,CACnC,KAAK,EAAE,cAAc,EACrB,OAAO,EAAE,WAAW,GACnB,OAAO,CAAC,UAAU,CAAC,CAuJrB"}

package/dist/tools/delete-doc.js

@@ -2,12 +2,13 @@
  * delete_doc tool - Delete documents with confirmation flow, soft delete to trash, and backup.
  */
 import { z } from 'zod';
-import { existsSync, readFileSync, mkdirSync, renameSync, unlinkSync } from 'fs';
+import { existsSync, readFileSync, mkdirSync, renameSync, unlinkSync, rmSync, statSync } from 'fs';
 import { join, dirname, basename, relative } from 'path';
 import { validatePath, isWritablePath, isProtectedPlanFile } from '../utils/paths.js';
 import { createBackup, formatTimestamp } from '../utils/backup.js';
 import { notFound, restrictedPath, DocumentError } from '../utils/errors.js';
-import { removeDocument } from '../indexer.js';
+import { removeDocument, removeDocumentsByPathPrefix } from '../indexer.js';
+import { getDocsRoot } from '../utils/repo-root.js';
 /**
  * Trash directory name (relative to repo root).
  */
@@ -31,12 +32,6 @@ export const DeleteDocInputSchema = z.object({
     confirm: z.boolean().optional().default(false),
     permanent: z.boolean().optional().default(false),
 });
-/**
- * Get repository root from config.
- */
-function getRepoRoot(config) {
-    return dirname(config.plansPath);
-}
 /**
  * Get the trash path for a file.
  */
@@ -70,7 +65,7 @@ function isProtectedFile(relativePath) {
  */
 export async function handleDeleteDoc(input, context) {
     const { path: inputPath, confirm, permanent } = input;
-    const repoRoot = getRepoRoot(context.config);
+    const repoRoot = getDocsRoot(context.config);
     try {
         // Validate the path
         const validated = validatePath(inputPath, repoRoot);
@@ -101,8 +96,13 @@ export async function handleDeleteDoc(input, context) {
         }
         // If no confirmation, return pending status with preview
         if (!confirm) {
-            const content = readFileSync(absolutePath, 'utf-8');
-            const preview = content.length > 500 ? content.substring(0, 500) + '...' : content;
+            const stats = statSync(absolutePath);
+            const preview = stats.isDirectory()
+                ? `Directory: ${inputPath}`
+                : (() => {
+                    const content = readFileSync(absolutePath, 'utf-8');
+                    return content.length > 500 ? content.substring(0, 500) + '...' : content;
+                })();
             const output = {
                 path: inputPath,
                 pending: true,
@@ -119,12 +119,23 @@ export async function handleDeleteDoc(input, context) {
         }
         // Create backup before deletion
         const backupResult = await createBackup(absolutePath, repoRoot);
+        const stats = statSync(absolutePath);
         // Remove from search index
-        await removeDocument(db, absolutePath);
+        if (stats.isDirectory()) {
+            await removeDocumentsByPathPrefix(db, absolutePath);
+        }
+        else {
+            await removeDocument(db, absolutePath);
+        }
         // Perform deletion
         if (permanent) {
-            // Permanent delete - just unlink the file
-            unlinkSync(absolutePath);
+            // Permanent delete - remove file or directory
+            if (stats.isDirectory()) {
+                rmSync(absolutePath, { recursive: true, force: true });
+            }
+            else {
+                unlinkSync(absolutePath);
+            }
             const output = {
                 path: inputPath,
                 deleted: true,
@@ -145,7 +156,7 @@ export async function handleDeleteDoc(input, context) {
             const trashDir = dirname(trashPath);
             // Ensure trash directory exists
             mkdirSync(trashDir, { recursive: true });
-            // Move file to trash
+            // Move file or directory to trash
             renameSync(absolutePath, trashPath);
             const output = {
                 path: inputPath,

package/dist/tools/delete-doc.js.map

@@ -1 +1 @@
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package/dist/tools/list-docs.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"list-docs.d.ts","sourceRoot":"","sources":["../../src/tools/list-docs.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAKxB,OAAO,KAAK,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,aAAa,CAAC;AAK3D;;GAEG;AACH,eAAO,MAAM,mBAAmB;;;;;;iBAS9B,CAAC;AAEH,MAAM,MAAM,aAAa,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,mBAAmB,CAAC,CAAC;AAEhE;;GAEG;AACH,MAAM,WAAW,QAAQ;IACvB,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,GAAG,WAAW,CAAC;IAC3B,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED;;GAEG;AACH,MAAM,WAAW,cAAc;IAC7B,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,QAAQ,EAAE,CAAC;IACpB,KAAK,EAAE,MAAM,CAAC;CACf;AAoHD;;;;;;;GAOG;AACH,wBAAsB,cAAc,CAClC,KAAK,EAAE,aAAa,EACpB,OAAO,EAAE,WAAW,GACnB,OAAO,CAAC,UAAU,CAAC,CA8GrB"}

package/dist/tools/list-docs.js

@@ -4,10 +4,11 @@
 import { z } from 'zod';
 import { readdir, lstat } from 'fs/promises';
 import { existsSync } from 'fs';
-import { join, dirname } from 'path';
+import { join } from 'path';
 import micromatch from 'micromatch';
 import { validatePath } from '../utils/paths.js';
 import { notFound } from '../utils/errors.js';
+import { getListingRoot } from '../utils/repo-root.js';
 /**
  * Input schema for list_docs tool.
  */
@@ -21,18 +22,6 @@ export const ListDocsInputSchema = z.object({
         .default(false)
         .describe('Format JSON response with indentation (default: false)'),
 });
-/**
- * Get repository root from config.
- * Uses the first docsPath entry as the repo root, or derives from plansPath.
- */
-function getRepoRoot(config) {
-    // Prefer docsPaths[0] if it exists (it's the repo root)
-    if (config.docsPaths && config.docsPaths.length > 0) {
-        return config.docsPaths[0];
-    }
-    // Fallback: use plansPath parent directory
-    return dirname(config.plansPath);
-}
 /**
  * Check if a name matches a glob pattern.
  */
@@ -139,7 +128,7 @@ export async function handleListDocs(input, context) {
     const { config } = context;
     try {
         // Get repo root
-        const repoRoot = getRepoRoot(config);
+        const repoRoot = getListingRoot(config);
         // Validate path (for directory, we allow empty string for root)
         const dirPath = path || '';
         let validated;

package/dist/tools/list-docs.js.map

@@ -1 +1 @@
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package/dist/tools/manage-tags.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"manage-tags.d.ts","sourceRoot":"","sources":["../../src/tools/manage-tags.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAOxB,OAAO,KAAK,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,aAAa,CAAC;AAE3D;;GAEG;AACH,eAAO,MAAM,qBAAqB;;;;;;;;;iBAWhC,CAAC;AAEH,MAAM,MAAM,eAAe,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,qBAAqB,CAAC,CAAC;AAEpE;;GAEG;AACH,MAAM,WAAW,gBAAgB;IAC/B,IAAI,EAAE,MAAM,CAAC;IACb,SAAS,EAAE,KAAK,GAAG,QAAQ,GAAG,MAAM,CAAC;IACrC,IAAI,EAAE,MAAM,EAAE,CAAC;IACf,OAAO,EAAE,OAAO,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAsCD;;;;;;GAMG;AACH,wBAAsB,gBAAgB,CACpC,KAAK,EAAE,eAAe,EACtB,OAAO,EAAE,WAAW,GACnB,OAAO,CAAC,UAAU,CAAC,CAkKrB"}
+{"version":3,"file":"manage-tags.d.ts","sourceRoot":"","sources":["../../src/tools/manage-tags.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAOxB,OAAO,KAAK,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,aAAa,CAAC;AAE3D;;GAEG;AACH,eAAO,MAAM,qBAAqB;;;;;;;;;iBAWhC,CAAC;AAEH,MAAM,MAAM,eAAe,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,qBAAqB,CAAC,CAAC;AAEpE;;GAEG;AACH,MAAM,WAAW,gBAAgB;IAC/B,IAAI,EAAE,MAAM,CAAC;IACb,SAAS,EAAE,KAAK,GAAG,QAAQ,GAAG,MAAM,CAAC;IACrC,IAAI,EAAE,MAAM,EAAE,CAAC;IACf,OAAO,EAAE,OAAO,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AA+BD;;;;;;GAMG;AACH,wBAAsB,gBAAgB,CACpC,KAAK,EAAE,eAAe,EACtB,OAAO,EAAE,WAAW,GACnB,OAAO,CAAC,UAAU,CAAC,CAkKrB"}

package/dist/tools/manage-tags.js

@@ -4,11 +4,11 @@
  */
 import { z } from 'zod';
 import { existsSync, readFileSync, writeFileSync } from 'fs';
-import { dirname } from 'path';
 import { validatePath } from '../utils/paths.js';
 import { notFound } from '../utils/errors.js';
 import { FrontmatterHandler } from '../utils/frontmatter.js';
 import { indexDocument } from '../indexer.js';
+import { getDocsRoot } from '../utils/repo-root.js';
 /**
  * Input schema for manage_tags tool.
  */
@@ -24,12 +24,6 @@ export const ManageTagsInputSchema = z.object({
         .default(false)
         .describe('Format JSON response with indentation (default: false)'),
 });
-/**
- * Get repository root from config.
- */
-function getRepoRoot(config) {
-    return dirname(config.plansPath);
-}
 /**
  * Extract tags from frontmatter and inline content.
  *
@@ -65,7 +59,7 @@ function extractAllTags(content, frontmatterHandler) {
  */
 export async function handleManageTags(input, context) {
     const { path, operation, tags = [], prettyPrint } = input;
-    const repoRoot = getRepoRoot(context.config);
+    const repoRoot = getDocsRoot(context.config);
     const frontmatterHandler = new FrontmatterHandler();
     try {
         // Validate path