kontexta-mcp 2.0.8 → 3.0.0

package/dist/agent-rules/rules-block.md

@@ -161,4 +161,5 @@ The matrix below is grouped by intent. For each tool: when to reach for it, the
 |---|---|---|---|
 | `register_project` | Register a new project root with kontexta | Already registered | `list_projects` |
 | `onboard_agent` | Write/update the rules block in CLAUDE.md / AGENTS.md / etc. | Editing regular project content | `update_file` |
+| `transfer_agent_context` | Copy CLAUDE.md / AGENTS.md / `.cursor/rules/*.mdc` etc. from the project repo into Kontexta's KB. Originals are NEVER deleted by this tool. | User wants files to stay in the repo (default) | `register_project` (which keeps files in place) |
 <!-- END kontexta:rules v{{VERSION}} -->

package/dist/index.js

@@ -57,6 +57,14 @@ function defaultDataDir() {
 function isWebContext() {
   return process.env.npm_package_name === "kxta-web" || !!process.env.NEXT_RUNTIME || !!process.env.__NEXT_PAGES_DIR;
 }
+function isTempOrTestPath(p) {
+  const lower = p.toLowerCase();
+  const tmp = os.tmpdir().toLowerCase();
+  return lower.startsWith("/tmp") || lower.startsWith(tmp) || lower.includes(`${path.sep}tmp${path.sep}`) || lower.includes("test") || lower.includes("-tmp-") || process.platform === "win32" && lower.includes("\\temp\\");
+}
+function resetDataDirCache() {
+  _resolvedDataDir = null;
+}
 function getDataDir() {
   if (_resolvedDataDir)
     return _resolvedDataDir;
@@ -66,31 +74,40 @@ function getDataDir() {
   const isWeb = isWebContext();
   if (isWeb && envOverride) {
     _resolvedDataDir = path.resolve(envOverride);
-    try {
-      fs.writeFileSync(cacheFile, _resolvedDataDir, "utf8");
-    } catch {
+    if (!isTempOrTestPath(_resolvedDataDir)) {
+      try {
+        fs.writeFileSync(cacheFile, _resolvedDataDir, "utf8");
+      } catch {
+      }
     }
     return _resolvedDataDir;
   }
-  const isTest = !!process.env.VITEST || process.env.NODE_ENV === "test" || envOverride && (envOverride.includes("test") || envOverride.includes("tmp"));
-  if (!isTest && fs.existsSync(cacheFile)) {
+  if (envOverride) {
+    _resolvedDataDir = path.resolve(envOverride);
+    const isTestEnv2 = !!process.env.VITEST || process.env.NODE_ENV === "test";
+    if (!isTempOrTestPath(_resolvedDataDir) && !isTestEnv2) {
+      try {
+        fs.writeFileSync(cacheFile, _resolvedDataDir, "utf8");
+      } catch {
+      }
+    }
+    return _resolvedDataDir;
+  }
+  const isTestEnv = !!process.env.VITEST || process.env.NODE_ENV === "test";
+  if (!isTestEnv && fs.existsSync(cacheFile)) {
     try {
       const cached = fs.readFileSync(cacheFile, "utf8").trim();
-      if (cached && path.isAbsolute(cached)) {
+      if (cached && path.isAbsolute(cached) && !isTempOrTestPath(cached)) {
         _resolvedDataDir = cached;
         return _resolvedDataDir;
       }
+      try {
+        fs.unlinkSync(cacheFile);
+      } catch {
+      }
     } catch {
     }
   }
-  if (envOverride) {
-    _resolvedDataDir = path.resolve(envOverride);
-    try {
-      fs.writeFileSync(cacheFile, _resolvedDataDir, "utf8");
-    } catch {
-    }
-    return _resolvedDataDir;
-  }
   _resolvedDataDir = defaultDataDir();
   return _resolvedDataDir;
 }
@@ -149,7 +166,7 @@ __export(safety_exports, {
   track: () => track,
   withLock: () => withLock
 });
-import { resolve as resolve2, sep, isAbsolute as isAbsolute2 } from "path";
+import { resolve as resolve2, sep as sep2, isAbsolute as isAbsolute2 } from "path";
 import { AsyncLocalStorage } from "async_hooks";
 function assertPathInside(base3, name50) {
   if (typeof name50 !== "string" || name50.length === 0) {
@@ -163,7 +180,7 @@ function assertPathInside(base3, name50) {
   }
   const baseResolved = resolve2(base3);
   const target = resolve2(baseResolved, name50);
-  if (target !== baseResolved && !target.startsWith(baseResolved + sep)) {
+  if (target !== baseResolved && !target.startsWith(baseResolved + sep2)) {
     throw new Error("Invalid path: escapes base directory");
   }
   return target;
@@ -420,8 +437,8 @@ var init_extensions = __esm({
 // ../../packages/core/dist/git/index.js
 import { createHash } from "crypto";
 import simpleGit from "simple-git";
-import { readFileSync as readFileSync3, writeFileSync as writeFileSync2, copyFileSync, mkdirSync as mkdirSync3, existsSync as existsSync3, rmSync, readdirSync as readdirSync2, statSync, lstatSync, unlinkSync, renameSync } from "fs";
-import { join as join3, relative, dirname as dirname2, isAbsolute as isAbsolute3, resolve as resolve3, sep as sep2 } from "path";
+import { readFileSync as readFileSync3, writeFileSync as writeFileSync2, copyFileSync, mkdirSync as mkdirSync3, existsSync as existsSync3, rmSync, readdirSync as readdirSync2, statSync, lstatSync, unlinkSync as unlinkSync2, renameSync } from "fs";
+import { join as join3, relative, dirname as dirname2, isAbsolute as isAbsolute3, resolve as resolve3, sep as sep3 } from "path";
 import { spawnSync } from "child_process";
 function redactCredentials(s3) {
   return s3.replace(/([a-z][a-z0-9+.-]*:\/\/)([^:@\/\s]+:[^@\/\s]+)@/gi, "$1***:***@");
@@ -540,7 +557,7 @@ async function restoreVersion(repoDir, filePath, commitHash) {
       renameSync(tmpPath, filePath);
     } catch (e3) {
       try {
-        unlinkSync(tmpPath);
+        unlinkSync2(tmpPath);
       } catch {
       }
       throw e3;
@@ -818,7 +835,7 @@ async function _syncBackupLocked(projectId, dataDir2, onStage) {
           }
         } else if (!expectedBackupPaths.has(fullPath)) {
           try {
-            unlinkSync(fullPath);
+            unlinkSync2(fullPath);
           } catch {
           }
         }
@@ -888,7 +905,7 @@ async function _syncBackupLocked(projectId, dataDir2, onStage) {
       if (project.path) {
         const localAbsolutePath = join3(project.path, relativePath);
         const projectResolved = resolve3(project.path);
-        if (resolve3(localAbsolutePath) !== projectResolved && !resolve3(localAbsolutePath).startsWith(projectResolved + sep2)) {
+        if (resolve3(localAbsolutePath) !== projectResolved && !resolve3(localAbsolutePath).startsWith(projectResolved + sep3)) {
           continue;
         }
         mkdirSync3(dirname2(localAbsolutePath), { recursive: true });
@@ -954,12 +971,12 @@ async function _syncBackupLocked(projectId, dataDir2, onStage) {
           continue;
         const localAbsolutePath = join3(project.path, insideBackup);
         const resolvedLocal = resolve3(localAbsolutePath);
-        if (resolvedLocal !== projectResolved && !resolvedLocal.startsWith(projectResolved + sep2)) {
+        if (resolvedLocal !== projectResolved && !resolvedLocal.startsWith(projectResolved + sep3)) {
           continue;
         }
         try {
           if (existsSync3(localAbsolutePath)) {
-            unlinkSync(localAbsolutePath);
+            unlinkSync2(localAbsolutePath);
           }
         } catch (e3) {
           console.warn(`syncBackup: failed to remove ${localAbsolutePath}:`, e3);
@@ -1001,8 +1018,8 @@ var init_git = __esm({
 
 // ../../packages/core/dist/files/index.js
 import { createHash as createHash2 } from "crypto";
-import { readFileSync as readFileSync4, writeFileSync as writeFileSync3, unlinkSync as unlinkSync2, renameSync as renameSync2, mkdirSync as mkdirSync4, readdirSync as readdirSync3, lstatSync as lstatSync2, existsSync as existsSync4, rmSync as rmSync2 } from "fs";
-import { join as join4, dirname as dirname3, resolve as resolve4, sep as sep3, isAbsolute as isAbsolute4 } from "path";
+import { readFileSync as readFileSync4, writeFileSync as writeFileSync3, unlinkSync as unlinkSync3, renameSync as renameSync2, mkdirSync as mkdirSync4, readdirSync as readdirSync3, lstatSync as lstatSync2, existsSync as existsSync4, rmSync as rmSync2 } from "fs";
+import { join as join4, dirname as dirname3, resolve as resolve4, sep as sep4, isAbsolute as isAbsolute4 } from "path";
 function listProjectFolders(projectPath) {
   const folders = [];
   function scan(dir, currentRel) {
@@ -1031,6 +1048,47 @@ function listProjectFolders(projectPath) {
   }
   return folders;
 }
+function listProjectFoldersWithFiles(projectPath) {
+  const folderFileCount = /* @__PURE__ */ new Map();
+  function scan(dir, currentRel) {
+    const entries = readdirSync3(dir);
+    for (const entry of entries) {
+      if (entry.startsWith(".") || entry === "node_modules")
+        continue;
+      const fullPath = join4(dir, entry);
+      const relPath = currentRel ? join4(currentRel, entry) : entry;
+      try {
+        const lst = lstatSync2(fullPath);
+        if (lst.isSymbolicLink())
+          continue;
+        if (lst.isDirectory()) {
+          scan(fullPath, relPath);
+        } else if (lst.isFile()) {
+          const ext = entry.endsWith(".mmd") ? ".mmd" : entry.endsWith(".md") ? ".md" : "";
+          if (ext) {
+            const parts = relPath.split("/");
+            for (let i4 = 0; i4 < parts.length - 1; i4++) {
+              const ancestor = parts.slice(0, i4 + 1).join("/");
+              folderFileCount.set(ancestor, (folderFileCount.get(ancestor) ?? 0) + 1);
+            }
+          }
+        }
+      } catch (e3) {
+      }
+    }
+  }
+  try {
+    scan(projectPath, "");
+  } catch (e3) {
+    console.error("Failed to scan project folders with files:", e3);
+  }
+  const result = [];
+  for (const [folder, count] of folderFileCount.entries()) {
+    if (count > 0)
+      result.push(folder);
+  }
+  return result.sort();
+}
 function computeHash(content) {
   return createHash2("sha256").update(content, "utf8").digest("hex");
 }
@@ -1137,7 +1195,7 @@ async function createFile(opts) {
         }
       } else {
         try {
-          unlinkSync2(filePath);
+          unlinkSync3(filePath);
         } catch {
         }
       }
@@ -1255,11 +1313,11 @@ function deleteFile(id, dataDir2) {
   if (file && dataDir2) {
     const knowledgeRoot = resolve4(dataDir2, "knowledge");
     const filePathResolved = isAbsolute4(file.path) ? file.path : resolve4(dataDir2, file.path);
-    const inKnowledge = filePathResolved === knowledgeRoot || filePathResolved.startsWith(knowledgeRoot + sep3);
+    const inKnowledge = filePathResolved === knowledgeRoot || filePathResolved.startsWith(knowledgeRoot + sep4);
     if (file.project_id === null && inKnowledge) {
       try {
         if (existsSync4(filePathResolved)) {
-          unlinkSync2(filePathResolved);
+          unlinkSync3(filePathResolved);
         }
       } catch (e3) {
         console.error("Failed to delete Knowledge Base file from disk:", e3);
@@ -1316,9 +1374,15 @@ function listFiles(opts) {
     }
     if (filters.folder !== void 0) {
       const segment = escapeLike(filters.folder);
-      sql += " AND (path LIKE ? ESCAPE '\\' OR path LIKE ? ESCAPE '\\')";
-      params.push(`%/${segment}/%`);
-      params.push(`%\\${segment}\\%`);
+      if (filters.project_path) {
+        sql += " AND (path LIKE ? ESCAPE '\\' OR path LIKE ? ESCAPE '\\')";
+        params.push(`${filters.project_path}/${segment}/%`);
+        params.push(`${filters.project_path}\\${segment}\\%`);
+      } else {
+        sql += " AND (path LIKE ? ESCAPE '\\' OR path LIKE ? ESCAPE '\\')";
+        params.push(`%/${segment}/%`);
+        params.push(`%\\${segment}\\%`);
+      }
     }
   }
   sql += " ORDER BY updated_at DESC";
@@ -1565,27 +1629,33 @@ function registerProject(name50, path3, description, remoteUrl) {
   `);
   const absolutePath = resolve5(path3);
   const result = insertStmt.run(name50, slug, absolutePath, description || null, remoteUrl || null);
+  let projectId;
   if (result.changes > 0) {
-    const projectId = Number(result.lastInsertRowid);
-    return db2.prepare("SELECT * FROM projects WHERE id = ?").get(projectId);
-  }
-  const byName = db2.prepare("SELECT * FROM projects WHERE name = ?").get(name50);
-  const bySlug = db2.prepare("SELECT * FROM projects WHERE slug = ?").get(slug);
-  const existing = byName ?? bySlug;
-  if (!existing) {
-    throw new Error(`registerProject: insert ignored but no matching project found for name='${name50}'`);
-  }
-  if (existing.path !== absolutePath) {
-    const conflicts = [];
-    if (byName)
-      conflicts.push(`name conflicts with '${byName.name}' at '${byName.path}'`);
-    if (bySlug && bySlug.id !== byName?.id)
-      conflicts.push(`slug '${slug}' conflicts with '${bySlug.name}' at '${bySlug.path}'`);
-    const err = new Error(`Cannot register '${name50}' at '${path3}': ${conflicts.join("; ")}. Pick a different name or unregister the existing project first.`);
-    err.code = "PROJECT_CONFLICT";
-    throw err;
-  }
-  return existing;
+    projectId = Number(result.lastInsertRowid);
+  } else {
+    const byName = db2.prepare("SELECT * FROM projects WHERE name = ?").get(name50);
+    const bySlug = db2.prepare("SELECT * FROM projects WHERE slug = ?").get(slug);
+    const existing = byName ?? bySlug;
+    if (!existing) {
+      throw new Error(`registerProject: insert ignored but no matching project found for name='${name50}'`);
+    }
+    if (existing.path !== absolutePath) {
+      const conflicts = [];
+      if (byName)
+        conflicts.push(`name conflicts with '${byName.name}' at '${byName.path}'`);
+      if (bySlug && bySlug.id !== byName?.id)
+        conflicts.push(`slug '${slug}' conflicts with '${bySlug.name}' at '${bySlug.path}'`);
+      const err = new Error(`Cannot register '${name50}' at '${path3}': ${conflicts.join("; ")}. Pick a different name or unregister the existing project first.`);
+      err.code = "PROJECT_CONFLICT";
+      throw err;
+    }
+    projectId = existing.id;
+  }
+  const newlyIndexed = reconcileIndex({ projectId, dataDir: getDataDir() }).newRecords.length;
+  return {
+    ...db2.prepare("SELECT * FROM projects WHERE id = ?").get(projectId),
+    newlyIndexed
+  };
 }
 function unregisterProject(projectId, dataDir2) {
   const db2 = getDatabase();
@@ -1661,9 +1731,14 @@ function reconcileIndex(opts) {
     } catch (e3) {
       if (isTopLevel) {
         if (typeof projectId === "number") {
-          throw new Error(`Failed to read project root ${dir}: ${e3?.message ?? e3}`);
+          if (e3?.code === "ENOENT") {
+            console.warn(`reconcileIndex: project root does not exist yet: ${dir}`);
+          } else {
+            throw new Error(`Failed to read project root ${dir}: ${e3?.message ?? e3}`);
+          }
+        } else {
+          console.warn(`reconcileIndex: failed to read KB root ${dir}: ${e3?.message ?? e3}`);
         }
-        console.warn(`reconcileIndex: failed to read KB root ${dir}: ${e3?.message ?? e3}`);
       }
       return;
     }
@@ -1758,7 +1833,9 @@ function reconcileIndex(opts) {
   return { scope, newly_indexed, refreshed, pruned, newRecords };
 }
 function discoverFiles(projectId, dataDir2) {
-  return reconcileIndex({ projectId, dataDir: dataDir2 }).newRecords;
+  reconcileIndex({ projectId, dataDir: dataDir2 });
+  const db2 = getDatabase();
+  return db2.prepare("SELECT * FROM files WHERE project_id = ? ORDER BY path").all(projectId);
 }
 function getTagsForFiles(fileIds) {
   const out = /* @__PURE__ */ new Map();
@@ -1805,6 +1882,7 @@ var init_metadata = __esm({
     init_safety();
     init_files();
     init_extensions();
+    init_paths();
     FtsQueryError = class extends Error {
       code = "FTS_PARSE";
       constructor(message) {
@@ -1862,8 +1940,8 @@ var init_settings = __esm({
 });
 
 // ../../packages/core/dist/agent-rules/index.js
-import { lstatSync as lstatSync4, readdirSync as readdirSync5, mkdirSync as mkdirSync5, writeFileSync as writeFileSync4, readFileSync as readFileSync6, renameSync as renameSync3, unlinkSync as unlinkSync3, existsSync as existsSync6 } from "fs";
-import { join as join6, sep as sep4, dirname as dirname4, isAbsolute as isAbsolute5 } from "path";
+import { lstatSync as lstatSync4, readdirSync as readdirSync5, mkdirSync as mkdirSync5, writeFileSync as writeFileSync4, readFileSync as readFileSync6, renameSync as renameSync3, unlinkSync as unlinkSync4, existsSync as existsSync6 } from "fs";
+import { join as join6, sep as sep5, dirname as dirname4, isAbsolute as isAbsolute5 } from "path";
 import { fileURLToPath as fileURLToPath2 } from "url";
 function loadCorePackageVersion() {
   try {
@@ -1926,7 +2004,7 @@ function isRegularNonSymlink(absPath) {
   }
 }
 function toForwardSlashes(p) {
-  return sep4 === "/" ? p : p.split(sep4).join("/");
+  return sep5 === "/" ? p : p.split(sep5).join("/");
 }
 function detectAgentContextFiles(projectPath) {
   const out = [];
@@ -1975,8 +2053,8 @@ function parseMarker(content) {
 function injectOrUpdate(content, block, version2) {
   const parsed = parseMarker(content);
   if (parsed === null) {
-    const sep9 = content.length === 0 ? "" : content.endsWith("\n\n") ? "" : content.endsWith("\n") ? "\n" : "\n\n";
-    return { action: "updated", content: content + sep9 + block };
+    const sep10 = content.length === 0 ? "" : content.endsWith("\n\n") ? "" : content.endsWith("\n") ? "\n" : "\n\n";
+    return { action: "updated", content: content + sep10 + block };
   }
   if (parsed.kind === "malformed") {
     throw new InjectError("malformed", "kontexta rules marker is malformed (BEGIN with no matching END)");
@@ -1999,7 +2077,7 @@ function atomicWrite(absPath, content) {
     renameSync3(tmp, absPath);
   } catch (e3) {
     try {
-      unlinkSync3(tmp);
+      unlinkSync4(tmp);
     } catch {
     }
     throw e3;
@@ -130556,7 +130634,7 @@ var init_dist3 = __esm({
   }
 });
 
-// ../../node_modules/.pnpm/@csstools+css-calc@3.2.1_@csstools+css-parser-algorithms@4.0.0_@csstools+css-tokenizer@4.0.0__5q6mm7d5muktbf6idkt2s7pica/node_modules/@csstools/css-calc/dist/index.mjs
+// ../../node_modules/.pnpm/@csstools+css-calc@3.2.1_@csstools+css-parser-algorithms@4.0.0_@csstools+css-tokenizer@_3b33f237655dfa7a35d4b0433ee15cf1/node_modules/@csstools/css-calc/dist/index.mjs
 function toLowerCaseAZ(e3) {
   return e3.replace(M, (e4) => String.fromCharCode(e4.charCodeAt(0) + 32));
 }
@@ -131315,7 +131393,7 @@ function replaceComponentValues2(n3, r5) {
 }
 var ParseError2, ParseErrorWithComponentValues, y, M, T, x, P, k, W, O, U, L, $2, V, Z, z, q, G, R, j, Y, _, H, J, K, Q;
 var init_dist4 = __esm({
-  "../../node_modules/.pnpm/@csstools+css-calc@3.2.1_@csstools+css-parser-algorithms@4.0.0_@csstools+css-tokenizer@4.0.0__5q6mm7d5muktbf6idkt2s7pica/node_modules/@csstools/css-calc/dist/index.mjs"() {
+  "../../node_modules/.pnpm/@csstools+css-calc@3.2.1_@csstools+css-parser-algorithms@4.0.0_@csstools+css-tokenizer@_3b33f237655dfa7a35d4b0433ee15cf1/node_modules/@csstools/css-calc/dist/index.mjs"() {
     "use strict";
     init_dist3();
     init_dist2();
@@ -132439,7 +132517,7 @@ var init_dist5 = __esm({
   }
 });
 
-// ../../node_modules/.pnpm/@csstools+css-color-parser@4.1.1_@csstools+css-parser-algorithms@4.0.0_@csstools+css-tokenize_2jw36v2skt7mvdil6fqdameniu/node_modules/@csstools/css-color-parser/dist/index.mjs
+// ../../node_modules/.pnpm/@csstools+css-color-parser@4.1.1_@csstools+css-parser-algorithms@4.0.0_@csstools+css-to_402b4b31fb8b001854d943f6a3e18a48/node_modules/@csstools/css-color-parser/dist/index.mjs
 function convertNaNToZero(e3) {
   return [Number.isNaN(e3[0]) ? 0 : e3[0], Number.isNaN(e3[1]) ? 0 : e3[1], Number.isNaN(e3[2]) ? 0 : e3[2]];
 }
@@ -133504,7 +133582,7 @@ function color(e3) {
 }
 var he, me, pe, Ne, be, ge, ve, fe, ye;
 var init_dist6 = __esm({
-  "../../node_modules/.pnpm/@csstools+css-color-parser@4.1.1_@csstools+css-parser-algorithms@4.0.0_@csstools+css-tokenize_2jw36v2skt7mvdil6fqdameniu/node_modules/@csstools/css-color-parser/dist/index.mjs"() {
+  "../../node_modules/.pnpm/@csstools+css-color-parser@4.1.1_@csstools+css-parser-algorithms@4.0.0_@csstools+css-to_402b4b31fb8b001854d943f6a3e18a48/node_modules/@csstools/css-color-parser/dist/index.mjs"() {
     "use strict";
     init_dist2();
     init_dist5();
@@ -137503,7 +137581,7 @@ var require_util7 = __commonJS({
       return path3;
     });
     exports.normalize = normalize3;
-    function join18(aRoot, aPath) {
+    function join17(aRoot, aPath) {
       if (aRoot === "") {
         aRoot = ".";
       }
@@ -137535,7 +137613,7 @@ var require_util7 = __commonJS({
       }
       return joined;
     }
-    exports.join = join18;
+    exports.join = join17;
     exports.isAbsolute = function(aPath) {
       return aPath.charAt(0) === "/" || urlRegexp.test(aPath);
     };
@@ -137749,7 +137827,7 @@ var require_util7 = __commonJS({
             parsed.path = parsed.path.substring(0, index + 1);
           }
         }
-        sourceURL = join18(urlGenerate(parsed), sourceURL);
+        sourceURL = join17(urlGenerate(parsed), sourceURL);
       }
       return normalize3(sourceURL);
     }
@@ -329707,17 +329785,17 @@ var init_whats_new = __esm({
 });
 
 // ../../packages/core/dist/project-map/index.js
-import { sep as sep5, join as join8, basename as basename2 } from "path";
+import { sep as sep6, join as join8, basename as basename2 } from "path";
 function emptyNode() {
   return { dirs: /* @__PURE__ */ new Map(), files: [] };
 }
 function stripRoot(filePath, root2) {
-  const rootWithSep = root2.endsWith(sep5) ? root2 : root2 + sep5;
+  const rootWithSep = root2.endsWith(sep6) ? root2 : root2 + sep6;
   if (filePath === root2)
     return [];
   if (!filePath.startsWith(rootWithSep))
     return null;
-  return filePath.slice(rootWithSep.length).split(sep5).filter(Boolean);
+  return filePath.slice(rootWithSep.length).split(sep6).filter(Boolean);
 }
 function locateFile(file, projectsById, dataDir2) {
   if (file.project_id == null) {
@@ -329860,73 +329938,6 @@ var init_project_map = __esm({
   }
 });
 
-// ../../packages/core/dist/compat/env-shim.js
-function migrateEnvVars() {
-  const migrated = [];
-  for (const [oldKey, newKey] of RENAMED_VARS) {
-    if (process.env[oldKey] && !process.env[newKey]) {
-      process.env[newKey] = process.env[oldKey];
-      migrated.push(oldKey);
-    }
-  }
-  if (migrated.length > 0) {
-    console.warn(`[Kontexta] Deprecated env vars migrated: ${migrated.join(", ")}. Rename to KONTEXTA_* prefix. Support removed in v2.0.`);
-  }
-  return migrated;
-}
-var RENAMED_VARS;
-var init_env_shim = __esm({
-  "../../packages/core/dist/compat/env-shim.js"() {
-    "use strict";
-    RENAMED_VARS = [
-      ["MNEXIS_DATA_DIR", "KONTEXTA_DATA_DIR"],
-      ["MNEXIS_DB_PATH", "KONTEXTA_DB_PATH"],
-      ["MNEXIS_WS_HOST", "KONTEXTA_WS_HOST"],
-      ["MNEXIS_WS_ORIGINS", "KONTEXTA_WS_ORIGINS"],
-      ["MNEXIS_WS_TOKEN", "KONTEXTA_WS_TOKEN"],
-      ["MNEXIS_EXPORT_MAX_BYTES", "KONTEXTA_EXPORT_MAX_BYTES"],
-      ["MNEXIS_INSTALL_HINT", "KONTEXTA_INSTALL_HINT"],
-      ["MNEXIS_PROJECT_TOKEN_WARN", "KONTEXTA_PROJECT_TOKEN_WARN"],
-      ["MNEXIS_SHUTDOWN_DRAIN_MS", "KONTEXTA_SHUTDOWN_DRAIN_MS"]
-    ];
-  }
-});
-
-// ../../packages/core/dist/compat/file-migration.js
-import { existsSync as existsSync7, renameSync as renameSync4, copyFileSync as copyFileSync2 } from "fs";
-import { join as join9 } from "path";
-function migrateDataFiles(dataDir2) {
-  for (const [oldName, newName] of DB_RENAMES) {
-    const oldPath = join9(dataDir2, oldName);
-    const newPath = join9(dataDir2, newName);
-    if (existsSync7(oldPath) && !existsSync7(newPath)) {
-      copyFileSync2(oldPath, oldPath + ".bak");
-      renameSync4(oldPath, newPath);
-      console.warn(`[Kontexta] Migrated ${oldName} \u2192 ${newName} (backup: ${oldName}.bak). Automatic migration removed in v2.0.`);
-    }
-  }
-}
-function migrateProjectConfig(projectRoot) {
-  const oldConfig = join9(projectRoot, "mnexis.json");
-  const newConfig = join9(projectRoot, "kontexta.json");
-  if (existsSync7(oldConfig) && !existsSync7(newConfig)) {
-    copyFileSync2(oldConfig, oldConfig + ".bak");
-    renameSync4(oldConfig, newConfig);
-    console.warn(`[Kontexta] Migrated mnexis.json \u2192 kontexta.json in ${projectRoot} (backup: mnexis.json.bak). Automatic migration removed in v2.0.`);
-  }
-}
-var DB_RENAMES;
-var init_file_migration = __esm({
-  "../../packages/core/dist/compat/file-migration.js"() {
-    "use strict";
-    DB_RENAMES = [
-      ["mnexis.db", "kontexta.db"],
-      ["mnexis.db-wal", "kontexta.db-wal"],
-      ["mnexis.db-shm", "kontexta.db-shm"]
-    ];
-  }
-});
-
 // ../../packages/core/dist/journal/types.js
 var init_types2 = __esm({
   "../../packages/core/dist/journal/types.js"() {
@@ -329936,7 +329947,7 @@ var init_types2 = __esm({
 
 // ../../packages/core/dist/journal/writer.js
 import { mkdirSync as mkdirSync6, openSync, closeSync, writeSync, fsyncSync } from "fs";
-import { join as join10, dirname as dirname5 } from "path";
+import { join as join9, dirname as dirname5 } from "path";
 var JournalWriter;
 var init_writer = __esm({
   "../../packages/core/dist/journal/writer.js"() {
@@ -329946,7 +329957,7 @@ var init_writer = __esm({
       currentDay = null;
       rawDir;
       constructor(opts) {
-        this.rawDir = join10(opts.baseDir, opts.projectSlug, "raw");
+        this.rawDir = join9(opts.baseDir, opts.projectSlug, "raw");
       }
       append(event) {
         const day = event.ts.slice(0, 10);
@@ -329968,7 +329979,7 @@ var init_writer = __esm({
           closeSync(this.fd);
           this.fd = null;
         }
-        const path3 = join10(this.rawDir, `${day}.jsonl`);
+        const path3 = join9(this.rawDir, `${day}.jsonl`);
         mkdirSync6(dirname5(path3), { recursive: true });
         this.fd = openSync(path3, "a");
         this.currentDay = day;
@@ -330023,14 +330034,14 @@ var init_redact = __esm({
 });
 
 // ../../packages/core/dist/journal/high-water.js
-import { readFileSync as readFileSync7, writeFileSync as writeFileSync5, renameSync as renameSync5, mkdirSync as mkdirSync7, existsSync as existsSync8 } from "fs";
-import { join as join11 } from "path";
+import { readFileSync as readFileSync7, writeFileSync as writeFileSync5, renameSync as renameSync4, mkdirSync as mkdirSync7, existsSync as existsSync7 } from "fs";
+import { join as join10 } from "path";
 function pathFor(baseDir, projectSlug2) {
-  return join11(baseDir, projectSlug2, ".distilled-up-to.json");
+  return join10(baseDir, projectSlug2, ".distilled-up-to.json");
 }
 function readHighWater(baseDir, projectSlug2) {
   const p = pathFor(baseDir, projectSlug2);
-  if (!existsSync8(p))
+  if (!existsSync7(p))
     return null;
   try {
     const raw = readFileSync7(p, "utf8");
@@ -330044,12 +330055,12 @@ function readHighWater(baseDir, projectSlug2) {
   }
 }
 function writeHighWater(baseDir, projectSlug2, hw) {
-  const dir = join11(baseDir, projectSlug2);
+  const dir = join10(baseDir, projectSlug2);
   mkdirSync7(dir, { recursive: true });
   const final = pathFor(baseDir, projectSlug2);
   const tmp = `${final}.tmp`;
   writeFileSync5(tmp, JSON.stringify(hw, null, 2));
-  renameSync5(tmp, final);
+  renameSync4(tmp, final);
 }
 var init_high_water = __esm({
   "../../packages/core/dist/journal/high-water.js"() {
@@ -330669,12 +330680,12 @@ var init_repository = __esm({
 });
 
 // ../../packages/core/dist/journal/cooldown.js
-import { existsSync as existsSync9, readFileSync as readFileSync8, writeFileSync as writeFileSync6, unlinkSync as unlinkSync4, mkdirSync as mkdirSync8 } from "fs";
-import { join as join12 } from "path";
+import { existsSync as existsSync8, readFileSync as readFileSync8, writeFileSync as writeFileSync6, unlinkSync as unlinkSync5, mkdirSync as mkdirSync8 } from "fs";
+import { join as join11 } from "path";
 function acquireCooldown(baseDir, projectSlug2, cooldownSeconds) {
-  mkdirSync8(join12(baseDir, projectSlug2), { recursive: true });
-  const lockPath = join12(baseDir, projectSlug2, ".distill.lock");
-  if (existsSync9(lockPath)) {
+  mkdirSync8(join11(baseDir, projectSlug2), { recursive: true });
+  const lockPath = join11(baseDir, projectSlug2, ".distill.lock");
+  if (existsSync8(lockPath)) {
     try {
       const ts = Number(readFileSync8(lockPath, "utf8"));
       if (!isNaN(ts) && Date.now() - ts < cooldownSeconds * 1e3)
@@ -330686,10 +330697,10 @@ function acquireCooldown(baseDir, projectSlug2, cooldownSeconds) {
   return true;
 }
 function releaseCooldown(baseDir, projectSlug2) {
-  const lockPath = join12(baseDir, projectSlug2, ".distill.lock");
-  if (existsSync9(lockPath)) {
+  const lockPath = join11(baseDir, projectSlug2, ".distill.lock");
+  if (existsSync8(lockPath)) {
     try {
-      unlinkSync4(lockPath);
+      unlinkSync5(lockPath);
     } catch {
     }
   }
@@ -330701,16 +330712,16 @@ var init_cooldown = __esm({
 });
 
 // ../../packages/core/dist/journal/distill.js
-import { readFileSync as readFileSync9, readdirSync as readdirSync6, existsSync as existsSync10, mkdirSync as mkdirSync9, writeFileSync as writeFileSync7 } from "fs";
-import { join as join13 } from "path";
+import { readFileSync as readFileSync9, readdirSync as readdirSync6, existsSync as existsSync9, mkdirSync as mkdirSync9, writeFileSync as writeFileSync7 } from "fs";
+import { join as join12 } from "path";
 function rawDir(opts) {
-  return join13(opts.dataDir, ...REL_BASE, opts.projectSlug, "raw");
+  return join12(opts.dataDir, ...REL_BASE, opts.projectSlug, "raw");
 }
 function distilledDir(opts, ts) {
-  return join13(opts.dataDir, ...REL_BASE, opts.projectSlug, ts.slice(0, 4), ts.slice(5, 7), ts.slice(8, 10));
+  return join12(opts.dataDir, ...REL_BASE, opts.projectSlug, ts.slice(0, 4), ts.slice(5, 7), ts.slice(8, 10));
 }
 async function distillJournal(opts) {
-  const cooldownBase = join13(opts.dataDir, ...REL_BASE);
+  const cooldownBase = join12(opts.dataDir, ...REL_BASE);
   const cooldownSec = opts.cooldownSeconds ?? 0;
   if (!acquireCooldown(cooldownBase, opts.projectSlug, cooldownSec)) {
     return {
@@ -330722,7 +330733,7 @@ async function distillJournal(opts) {
     };
   }
   try {
-    const hw = readHighWater(join13(opts.dataDir, ...REL_BASE), opts.projectSlug);
+    const hw = readHighWater(join12(opts.dataDir, ...REL_BASE), opts.projectSlug);
     const since = hw?.last_event_ts ?? "0000-01-01T00:00:00Z";
     const cutoff = new Date(opts.now.getTime() - opts.inFlightWindowSeconds * 1e3).toISOString();
     const events = readRawEvents(opts, since, cutoff, opts.maxEvents);
@@ -330738,7 +330749,7 @@ async function distillJournal(opts) {
       const dir = distilledDir(opts, lastEvent.ts);
       mkdirSync9(dir, { recursive: true });
       const filename = `task-${bucket.task_slug}.md`;
-      const filePath = join13(dir, filename);
+      const filePath = join12(dir, filename);
       const fm = buildFrontmatter2(bucket, opts.projectSlug);
       const entry = renderMechanicalEntry({
         task_slug: bucket.task_slug,
@@ -330746,7 +330757,7 @@ async function distillJournal(opts) {
         now: lastEvent.ts,
         extraPatterns: opts.extraPatterns
       });
-      if (existsSync10(filePath)) {
+      if (existsSync9(filePath)) {
         const existing = readFileSync9(filePath, "utf8");
         writeFileSync7(filePath, replaceOrAppendEntry(existing, fm, entry));
       } else {
@@ -330768,7 +330779,7 @@ async function distillJournal(opts) {
       });
     }
     const newHw = events[events.length - 1].ts;
-    writeHighWater(join13(opts.dataDir, ...REL_BASE), opts.projectSlug, {
+    writeHighWater(join12(opts.dataDir, ...REL_BASE), opts.projectSlug, {
       last_event_ts: newHw,
       last_distilled_at: opts.now.toISOString(),
       events_processed: (hw?.events_processed ?? 0) + events.length
@@ -330786,17 +330797,17 @@ async function distillJournal(opts) {
 }
 function readRawEvents(opts, sinceTs, untilTs, max2) {
   const dirs = [rawDir(opts)];
-  const defaultDir = join13(opts.dataDir, ...REL_BASE, "default", "raw");
-  if (defaultDir !== dirs[0] && existsSync10(defaultDir)) {
+  const defaultDir = join12(opts.dataDir, ...REL_BASE, "default", "raw");
+  if (defaultDir !== dirs[0] && existsSync9(defaultDir)) {
     dirs.push(defaultDir);
   }
   const out = [];
   for (const dir of dirs) {
-    if (!existsSync10(dir))
+    if (!existsSync9(dir))
       continue;
     const files = readdirSync6(dir).filter((f3) => f3.endsWith(".jsonl")).sort();
     for (const f3 of files) {
-      const lines = readFileSync9(join13(dir, f3), "utf8").split("\n").filter(Boolean);
+      const lines = readFileSync9(join12(dir, f3), "utf8").split("\n").filter(Boolean);
       for (const line of lines) {
         try {
           const ev = JSON.parse(line);
@@ -330983,17 +330994,17 @@ var init_git_watcher = __esm({
 });
 
 // ../../packages/core/dist/journal/presence.js
-import { readdirSync as readdirSync7, statSync as statSync3, existsSync as existsSync11 } from "fs";
-import { join as join14 } from "path";
+import { readdirSync as readdirSync7, statSync as statSync3, existsSync as existsSync10 } from "fs";
+import { join as join13 } from "path";
 function isMcpActive(baseDir, projectSlug2, windowSec) {
-  const rawDir2 = join14(baseDir, projectSlug2, "raw");
-  if (!existsSync11(rawDir2))
+  const rawDir2 = join13(baseDir, projectSlug2, "raw");
+  if (!existsSync10(rawDir2))
     return false;
   const cutoff = Date.now() - windowSec * 1e3;
   for (const f3 of readdirSync7(rawDir2)) {
     if (!f3.endsWith(".jsonl"))
       continue;
-    if (statSync3(join14(rawDir2, f3)).mtimeMs >= cutoff)
+    if (statSync3(join13(rawDir2, f3)).mtimeMs >= cutoff)
       return true;
   }
   return false;
@@ -331005,8 +331016,8 @@ var init_presence = __esm({
 });
 
 // ../../packages/core/dist/journal/housekeep.js
-import { readdirSync as readdirSync8, statSync as statSync4, unlinkSync as unlinkSync5, renameSync as renameSync6, mkdirSync as mkdirSync10, existsSync as existsSync12, readFileSync as readFileSync10 } from "fs";
-import { join as join15 } from "path";
+import { readdirSync as readdirSync8, statSync as statSync4, unlinkSync as unlinkSync6, renameSync as renameSync5, mkdirSync as mkdirSync10, existsSync as existsSync11, readFileSync as readFileSync10 } from "fs";
+import { join as join14 } from "path";
 function lastEventTs(path3) {
   try {
     const content = readFileSync10(path3, "utf8");
@@ -331030,12 +331041,12 @@ function housekeepJournal(cfg) {
   };
   if (cfg.retention.raw_days > 0) {
     const cutoff = now.getTime() - cfg.retention.raw_days * 864e5;
-    const rawDir2 = join15(cfg.baseDir, cfg.projectSlug, "raw");
-    if (existsSync12(rawDir2)) {
+    const rawDir2 = join14(cfg.baseDir, cfg.projectSlug, "raw");
+    if (existsSync11(rawDir2)) {
       const hw = readHighWater(cfg.baseDir, cfg.projectSlug);
       const highWaterTs = hw?.last_event_ts ?? null;
       for (const f3 of readdirSync8(rawDir2).filter((n3) => n3.endsWith(".jsonl"))) {
-        const p = join15(rawDir2, f3);
+        const p = join14(rawDir2, f3);
         if (statSync4(p).mtimeMs >= cutoff)
           continue;
         const fileLastTs = lastEventTs(p);
@@ -331043,7 +331054,7 @@ function housekeepJournal(cfg) {
           result.raw_files_skipped_undistilled++;
           continue;
         }
-        unlinkSync5(p);
+        unlinkSync6(p);
         result.raw_files_pruned++;
       }
     }
@@ -331057,12 +331068,12 @@ function housekeepJournal(cfg) {
       JOIN projects p ON p.id = jm.project_id
       WHERE p.slug = ? AND jm.last_active_at < ?
     `).all(cfg.projectSlug, archiveCutoff);
-    const archiveDir = join15(cfg.baseDir, cfg.projectSlug, "_archive");
+    const archiveDir = join14(cfg.baseDir, cfg.projectSlug, "_archive");
     mkdirSync10(archiveDir, { recursive: true });
     for (const row of cold) {
-      const dest = join15(archiveDir, row.path.split("/").pop() ?? `task-${row.file_id}.md`);
-      if (!existsSync12(dest) && existsSync12(row.path)) {
-        renameSync6(row.path, dest);
+      const dest = join14(archiveDir, row.path.split("/").pop() ?? `task-${row.file_id}.md`);
+      if (!existsSync11(dest) && existsSync11(row.path)) {
+        renameSync5(row.path, dest);
         db2.prepare(`UPDATE files SET path = ? WHERE id = ?`).run(dest, row.file_id);
         result.archived_tasks++;
       }
@@ -331215,13 +331226,11 @@ __export(dist_exports2, {
   journalRefsByValue: () => journalRefsByValue,
   listFiles: () => listFiles,
   listProjectFolders: () => listProjectFolders,
+  listProjectFoldersWithFiles: () => listProjectFoldersWithFiles,
   listProjects: () => listProjects,
   listTags: () => listTags,
   loadExtraPatterns: () => loadExtraPatterns,
   markUpgradeApplied: () => markUpgradeApplied,
-  migrateDataFiles: () => migrateDataFiles,
-  migrateEnvVars: () => migrateEnvVars,
-  migrateProjectConfig: () => migrateProjectConfig,
   moveFile: () => moveFile,
   openTasksForProject: () => openTasksForProject,
   parseMarker: () => parseMarker,
@@ -331236,6 +331245,7 @@ __export(dist_exports2, {
   removeTags: () => removeTags,
   renderMechanicalEntry: () => renderMechanicalEntry,
   replaceSection: () => replaceSection,
+  resetDataDirCache: () => resetDataDirCache,
   resolveSince: () => resolveSince,
   restoreVersion: () => restoreVersion,
   runPatterns: () => runPatterns,
@@ -331278,14 +331288,28 @@ var init_dist7 = __esm({
     init_clip();
     init_whats_new();
     init_project_map();
-    init_env_shim();
-    init_file_migration();
     init_journal();
   }
 });
 
+// src/re2-compat.ts
+import { createRequire as createRequire4 } from "module";
+var require5, RE2Class, re2_compat_default;
+var init_re2_compat = __esm({
+  "src/re2-compat.ts"() {
+    "use strict";
+    require5 = createRequire4(import.meta.url);
+    try {
+      RE2Class = require5("re2");
+    } catch (e3) {
+      console.warn("kontexta-mcp: Failed to load native 're2' module, falling back to standard RegExp.");
+      RE2Class = RegExp;
+    }
+    re2_compat_default = RE2Class;
+  }
+});
+
 // src/hands/sanitizer.ts
-import RE2 from "re2";
 function rejectNul(s3) {
   if (s3.includes("\0")) {
     throw new Error("NUL byte not permitted in param value");
@@ -331321,7 +331345,7 @@ function isLiteralArgv0(s3) {
 function compilePattern(src) {
   let r5;
   try {
-    r5 = new RE2(src);
+    r5 = new re2_compat_default(src);
   } catch (e3) {
     throw new Error(`invalid pattern: ${e3?.message ?? e3}`);
   }
@@ -331358,6 +331382,7 @@ var SAFE_INT_MIN, SAFE_INT_MAX, DEFAULT_STRING_PATTERN, MAX_STRING_LENGTH, CONTR
 var init_sanitizer = __esm({
   "src/hands/sanitizer.ts"() {
     "use strict";
+    init_re2_compat();
     SAFE_INT_MIN = Number.MIN_SAFE_INTEGER;
     SAFE_INT_MAX = Number.MAX_SAFE_INTEGER;
     DEFAULT_STRING_PATTERN = "^[^-\\s][^\\n\\r]*$";
@@ -331376,7 +331401,7 @@ __export(executor_exports, {
   resolveCwd: () => resolveCwd
 });
 import { spawn } from "child_process";
-import { resolve as resolvePath, sep as sep7 } from "path";
+import { resolve as resolvePath, sep as sep8 } from "path";
 import { realpathSync } from "fs";
 function resolveArgv(command, params, defs, argSeparator) {
   const resolvedValues = {};
@@ -331432,7 +331457,7 @@ function resolveCwd(projectRoot, workingDir) {
   } catch {
     throw new Error(`workingDir does not exist: ${workingDir}`);
   }
-  if (real !== rootReal && !real.startsWith(rootReal + sep7)) {
+  if (real !== rootReal && !real.startsWith(rootReal + sep8)) {
     throw new Error(`workingDir resolved outside project root`);
   }
   return real;
@@ -331596,12 +331621,13 @@ ${tailStr}`;
 
 // src/index.ts
 init_dist7();
+init_re2_compat();
 import { McpServer, ResourceTemplate } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
 import { z as z6 } from "zod";
-import RE22 from "re2";
-import { isAbsolute as isAbsolute7, join as join17, resolve as resolve7, sep as sep8, dirname as dirname6 } from "path";
-import { statSync as statSync5, openSync as openSync2, readSync, closeSync as closeSync2, readFileSync as readFileSync12, existsSync as existsSync14, realpathSync as realpathSync2 } from "fs";
+import { isAbsolute as isAbsolute7, join as join16, resolve as resolve7, sep as sep9, dirname as dirname6 } from "path";
+import { statSync as statSync5, lstatSync as lstatSync5, openSync as openSync2, readSync, closeSync as closeSync2, readFileSync as readFileSync12, existsSync as existsSync13, realpathSync as realpathSync2 } from "fs";
+import { createHash as createHash3 } from "crypto";
 import { fileURLToPath as fileURLToPath3 } from "url";
 
 // src/hands/registry.ts
@@ -331609,9 +331635,8 @@ import { z as z2 } from "zod";
 
 // src/hands/loader.ts
 init_sanitizer();
-init_dist7();
-import { readFileSync as readFileSync11, existsSync as existsSync13 } from "fs";
-import { join as join16, isAbsolute as isAbsolute6, normalize as normalize2, sep as sep6 } from "path";
+import { readFileSync as readFileSync11, existsSync as existsSync12 } from "fs";
+import { join as join15, isAbsolute as isAbsolute6, normalize as normalize2, sep as sep7 } from "path";
 var TOOL_NAME_RE = /^[a-z][a-z0-9-]*$/;
 var PARAM_NAME_RE = /^[a-zA-Z_][a-zA-Z0-9_]*$/;
 var FORBIDDEN_ENV = /* @__PURE__ */ new Set([
@@ -331628,9 +331653,8 @@ var TIMEOUT_DEFAULT = 6e4;
 var OUTPUT_MAX = 1e6;
 var OUTPUT_DEFAULT = 1e5;
 function loadProjectConfig(projectRoot) {
-  migrateProjectConfig(projectRoot);
-  const file = join16(projectRoot, "kontexta.json");
-  if (!existsSync13(file)) {
+  const file = join15(projectRoot, "kontexta.json");
+  if (!existsSync12(file)) {
     return { found: false, tools: {}, disabled: [], warnings: [], errors: [] };
   }
   let raw;
@@ -331680,7 +331704,7 @@ function validateTool(name50, def, projectRoot) {
   }
   if (!isLiteralArgv0(def.command[0])) return reject("argv[0] must be literal (no {{param}})");
   const argv0 = def.command[0];
-  if (!isAbsolute6(argv0) && (argv0.includes("/") || argv0.includes(sep6))) {
+  if (!isAbsolute6(argv0) && (argv0.includes("/") || argv0.includes(sep7))) {
     return reject("argv[0] must be absolute or a bare command name (no relative paths)");
   }
   const paramDefs = def.params ?? {};
@@ -331713,7 +331737,7 @@ function validateTool(name50, def, projectRoot) {
     if (typeof def.workingDir !== "string") return reject("workingDir must be string");
     if (isAbsolute6(def.workingDir)) return reject("workingDir must be relative");
     const norm = normalize2(def.workingDir);
-    if (norm.startsWith("..") || norm.split(sep6).includes("..")) return reject("workingDir must not contain ..");
+    if (norm.startsWith("..") || norm.split(sep7).includes("..")) return reject("workingDir must not contain ..");
   }
   if (def.env !== void 0) {
     if (typeof def.env !== "object" || def.env === null) return reject("env must be object");
@@ -332551,7 +332575,7 @@ function getAgentRulesWarning(projectId) {
     }
     const outdatedProjects = [];
     for (const p of projects) {
-      if (!p || !p.path || !existsSync14(p.path)) continue;
+      if (!p || !p.path || !existsSync13(p.path)) continue;
       const contextFiles = detectAgentContextFiles(p.path);
       if (contextFiles.length === 0) continue;
       const statuses = checkAgentRulesStatus(p.path, contextFiles);
@@ -332620,8 +332644,8 @@ var pkgVersionFound = false;
 try {
   let currentDir = dirname6(fileURLToPath3(import.meta.url));
   while (currentDir !== dirname6(currentDir)) {
-    const p = join17(currentDir, "package.json");
-    if (existsSync14(p)) {
+    const p = join16(currentDir, "package.json");
+    if (existsSync13(p)) {
       const pkg = JSON.parse(readFileSync12(p, "utf8"));
       if (pkg.name === "kontexta-mcp" && pkg.version) {
         pkgVersion = pkg.version;
@@ -332642,7 +332666,7 @@ var server = new McpServer({
   version: pkgVersion
 });
 var handsRegistry = new HandsRegistry(server);
-var baseJournalDir = join17(dataDir, "knowledge", "journal");
+var baseJournalDir = join16(dataDir, "knowledge", "journal");
 var projectSlug = process.env.KONTEXTA_DEFAULT_PROJECT_SLUG ?? "default";
 var agent = process.env.KONTEXTA_AGENT ?? "unknown";
 var sid = `${process.pid}-${Date.now().toString(36)}`;
@@ -332700,8 +332724,8 @@ server.tool(
       const journalFolder = "journal";
       const title = `journal-${today}`;
       const db2 = getDatabase();
-      const knowledgeDir = join17(dataDir, "knowledge");
-      const expectedPath = join17(knowledgeDir, journalFolder, `${title}.md`);
+      const knowledgeDir = join16(dataDir, "knowledge");
+      const expectedPath = join16(knowledgeDir, journalFolder, `${title}.md`);
       const existingRow = db2.prepare("SELECT id, path FROM files WHERE path = ? AND project_id IS NULL").get(expectedPath);
       if (existingRow) {
         const existing = readFile(existingRow.id);
@@ -332831,7 +332855,7 @@ server.tool(
           folder = parts.length > 1 ? parts.slice(0, -1).join("/") : null;
         }
       } else {
-        const knowledgeRoot = join17(dataDir, "knowledge");
+        const knowledgeRoot = join16(dataDir, "knowledge");
         if (file.path?.startsWith(knowledgeRoot)) {
           const rel = file.path.slice(knowledgeRoot.length).replace(/^[\/\\]+/, "");
           const parts = rel.split(/[\/\\]/);
@@ -332984,7 +333008,7 @@ server.tool(
     try {
       let re;
       try {
-        re = new RE22(pattern, case_insensitive ? "i" : "");
+        re = new re2_compat_default(pattern, case_insensitive ? "i" : "");
       } catch (e3) {
         throw new Error(`invalid regex: ${e3?.message ?? e3}`);
       }
@@ -333039,7 +333063,7 @@ server.tool(
     try {
       let re;
       try {
-        re = new RE22(pattern, case_insensitive ? "i" : "");
+        re = new re2_compat_default(pattern, case_insensitive ? "i" : "");
       } catch (e3) {
         throw new Error(`invalid regex: ${e3?.message ?? e3}`);
       }
@@ -333280,7 +333304,7 @@ server.tool(
   async () => {
     const result = listProjects();
     const augmented = result.map((p) => {
-      const has_hands = !!(p.path && existsSync14(p.path) && existsSync14(`${p.path}/kontexta.json`));
+      const has_hands = !!(p.path && existsSync13(p.path) && existsSync13(`${p.path}/kontexta.json`));
       const contextFiles = p.path ? detectAgentContextFiles(p.path) : [];
       const statuses = p.path ? checkAgentRulesStatus(p.path, contextFiles) : [];
       const outdated = statuses.filter((s3) => !s3.upToDate);
@@ -333488,6 +333512,130 @@ RETURNS: { written: [{ path, action: created|updated|skipped, version }], skippe
     }
   }
 );
+server.tool(
+  "transfer_agent_context",
+  `COPY existing agent context files (CLAUDE.md, AGENTS.md, .cursor/rules/*.mdc, etc.) from a project's repo into Kontexta's per-project knowledge base so they're indexed by FTS5 and can be git-synced through Kontexta's own backup engine.
+
+This tool ONLY COPIES. It never deletes or modifies the originals in your repo. After a successful transfer, the response includes the list of source paths so the user can manually remove them if desired. No tool argument, no flag, and no code path in this tool ever calls a destructive filesystem operation against \`project.path\`.
+
+MANDATORY: This tool writes new files into Kontexta's data dir. You MUST seek explicit user consent before calling. Set 'confirm: true' only after the user has agreed.
+
+PARAMETERS:
+- project_id: number, required. Project ID returned from register_project.
+- confirm: boolean, required. Must be true.
+- files: string[], optional. Project-relative paths to transfer. Omit or pass [] to transfer all detected agent context files (uses the same detection list as register_project / onboard_agent).
+
+RETURNS: { transferred: [{ source_path, kb_id, kb_path, est_tokens }], skipped: [{ source_path, reason }], next_action }
+Skip reasons: "missing" | "symlink" | "outside_project" | "already_transferred_same_content" | "read_error" | "write_error".
+
+IDEMPOTENT: re-running with the same files copies nothing if the content is unchanged \u2014 duplicate transfers are detected via SHA-256 hash comparison against existing project KB rows.`,
+  {
+    project_id: z6.number().describe("Project ID returned from register_project"),
+    confirm: z6.boolean().describe("MANDATORY: Set to true only after obtaining explicit user consent."),
+    files: z6.array(z6.string()).optional().describe("Project-relative paths to transfer. Omit to transfer all detected context files.")
+  },
+  async ({ project_id, confirm, files }) => {
+    try {
+      if (confirm !== true) {
+        return {
+          isError: true,
+          content: [{
+            type: "text",
+            text: JSON.stringify({
+              error: "User consent required",
+              details: "This tool copies project files into Kontexta's KB. Explain the proposed transfer to the user and obtain explicit consent, then re-run with 'confirm: true'. Originals in the project repo are NOT touched."
+            }, null, 2)
+          }]
+        };
+      }
+      const db2 = getDatabase();
+      const project = db2.prepare("SELECT id, name, slug, path FROM projects WHERE id = ?").get(project_id);
+      if (!project || !project.path) {
+        return {
+          isError: true,
+          content: [{ type: "text", text: JSON.stringify({ error: `Project ${project_id} not found or has no path` }, null, 2) }]
+        };
+      }
+      const projectPath = project.path;
+      const targetRels = files && files.length > 0 ? files : detectAgentContextFiles(projectPath);
+      const existingHashes = new Set(
+        db2.prepare("SELECT content_hash FROM files WHERE project_id = ? AND storage_type = 'local' AND content_hash IS NOT NULL").all(project.id).map((r5) => r5.content_hash)
+      );
+      const transferred = [];
+      const skipped = [];
+      for (const rel of targetRels) {
+        let abs2;
+        try {
+          abs2 = assertPathInside(projectPath, rel);
+        } catch {
+          skipped.push({ source_path: rel, reason: "outside_project" });
+          continue;
+        }
+        let stat;
+        try {
+          stat = lstatSync5(abs2);
+        } catch {
+          stat = null;
+        }
+        if (!stat) {
+          skipped.push({ source_path: rel, reason: "missing" });
+          continue;
+        }
+        if (stat.isSymbolicLink()) {
+          skipped.push({ source_path: rel, reason: "symlink" });
+          continue;
+        }
+        if (!stat.isFile()) {
+          skipped.push({ source_path: rel, reason: "missing" });
+          continue;
+        }
+        let content;
+        try {
+          content = readFileSync12(abs2, "utf8");
+        } catch {
+          skipped.push({ source_path: rel, reason: "read_error" });
+          continue;
+        }
+        const hash = createHash3("sha256").update(content, "utf8").digest("hex");
+        if (existingHashes.has(hash)) {
+          skipped.push({ source_path: rel, reason: "already_transferred_same_content" });
+          continue;
+        }
+        const titleSource = rel.replace(/\.[^./]+$/, "");
+        const title = titleSource || rel;
+        try {
+          const created = await createFile({
+            title,
+            content,
+            destination: "kontexta",
+            projectId: project.id,
+            folder: "agent-context",
+            dataDir,
+            sourcePath: abs2
+          });
+          existingHashes.add(hash);
+          transferred.push({
+            source_path: rel,
+            kb_id: created.id,
+            kb_path: created.path,
+            est_tokens: estimateTokensFromBuffer(Buffer.from(content, "utf8"))
+          });
+        } catch (e3) {
+          skipped.push({ source_path: rel, reason: `write_error: ${e3?.message ?? String(e3)}` });
+        }
+      }
+      const next_action = transferred.length > 0 ? `Copied ${transferred.length} file(s) into Kontexta's KB. Originals in your repo are unchanged. To remove them yourself: ${transferred.map((t3) => `rm "${join16(projectPath, t3.source_path)}"`).join(" && ")}` : "No files were transferred. See skipped[] for reasons.";
+      return {
+        content: [{ type: "text", text: JSON.stringify({ transferred, skipped, next_action }, null, 2) }]
+      };
+    } catch (e3) {
+      return {
+        isError: true,
+        content: [{ type: "text", text: JSON.stringify({ error: e3?.message ?? String(e3) }, null, 2) }]
+      };
+    }
+  }
+);
 server.tool(
   "commit_backup",
   "SIDE-EFFECTFUL \u2014 TOUCHES THE NETWORK. Sync the project's KB data into its git backup directory, create a commit, and `git push` to `origin`. AUTH: relies on the local user's git credentials (SSH agent, credential helper, etc.) \u2014 there is no in-server auth. Kontexta does not rate-limit, but the remote may. Idempotent in steady state: a no-op commit is skipped, but the push still runs. Throws if the project has no configured backup repo or if push fails (network, auth, conflict). Returns `{success, copied_files_count, copied_paths}`. Use after a batch of KB writes to get changes off-machine.",
@@ -333761,7 +333909,7 @@ server.tool(
 );
 function resolveFolderBase(projectId) {
   if (projectId === void 0 || projectId === null) {
-    return join17(dataDir, "knowledge");
+    return join16(dataDir, "knowledge");
   }
   const project = getDatabase().prepare("SELECT path FROM projects WHERE id = ?").get(projectId);
   if (!project?.path) {
@@ -333886,7 +334034,7 @@ server.tool(
         if (!project?.path) throw new Error(`Project not found for file ${file_id}`);
         base3 = project.path;
       } else {
-        base3 = join17(dataDir, "knowledge");
+        base3 = join16(dataDir, "knowledge");
       }
       let baseResolved;
       try {
@@ -333902,8 +334050,8 @@ server.tool(
       } catch {
         throw new Error(`Destination parent directory does not exist: ${destParent}`);
       }
-      const destResolved = join17(destParentReal, destAbs.slice(destParent.length + (destParent.endsWith(sep8) ? 0 : 1)));
-      if (destResolved !== baseResolved && !destResolved.startsWith(baseResolved + sep8)) {
+      const destResolved = join16(destParentReal, destAbs.slice(destParent.length + (destParent.endsWith(sep9) ? 0 : 1)));
+      if (destResolved !== baseResolved && !destResolved.startsWith(baseResolved + sep9)) {
         throw new Error(`new_path must be inside ${base3}`);
       }
       let srcResolved;
@@ -333912,7 +334060,7 @@ server.tool(
       } catch {
         srcResolved = resolve7(file.path);
       }
-      if (srcResolved !== baseResolved && !srcResolved.startsWith(baseResolved + sep8)) {
+      if (srcResolved !== baseResolved && !srcResolved.startsWith(baseResolved + sep9)) {
         throw new Error(`source path ${file.path} is no longer inside ${base3}; refusing to move`);
       }
       const updated = moveFile(file_id, new_path);
@@ -334607,7 +334755,7 @@ server.tool(
   "Re-scan every registered project's `kontexta.json` and rebuild the live Hands tool registry \u2014 newly-declared tools become callable immediately, removed tools disappear from `tools/list`. SIDE EFFECT is on the running MCP session's tool inventory only (no disk writes). Idempotent. No external auth or rate limits. Takes no parameters. Returns per-project load results (counts of registered/disabled tools and any validation warnings). Use after editing a `kontexta.json` mid-session; for the schema see `describe_hands_schema`.",
   {},
   async () => {
-    const projects = listProjects().filter((p) => p.path && existsSync14(p.path)).map((p) => ({ name: p.name, root: p.path }));
+    const projects = listProjects().filter((p) => p.path && existsSync13(p.path)).map((p) => ({ name: p.name, root: p.path }));
     const r5 = handsRegistry.reloadAll(projects);
     return { content: [{ type: "text", text: JSON.stringify(r5, null, 2) }] };
   }
@@ -334638,7 +334786,7 @@ server.tool(
 async function main() {
   const transport = new StdioServerTransport();
   {
-    const projects = listProjects().filter((p) => p.path && existsSync14(p.path)).map((p) => ({ name: p.name, root: p.path }));
+    const projects = listProjects().filter((p) => p.path && existsSync13(p.path)).map((p) => ({ name: p.name, root: p.path }));
     const r5 = handsRegistry.reloadAll(projects);
     console.error(
       `Kontexta Hands: loaded ${r5.perProject.length} projects, registered ${r5.totalRegistered} tools (${r5.totalDisabled} disabled)`

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "kontexta-mcp",
-  "version": "2.0.8",
+  "version": "3.0.0",
   "description": "The local Brain and Hands for AI coding agents (MCP Server)",
   "keywords": [
     "mcp",
@@ -38,7 +38,7 @@
     "./hands/types": "./dist/hands/types.js"
   },
   "engines": {
-    "node": ">=20"
+    "node": ">=22"
   },
   "files": [
     "dist",
@@ -61,7 +61,7 @@
   },
   "dependencies": {
     "@modelcontextprotocol/sdk": "^1.12.0",
-    "better-sqlite3": "^11.7.0",
+    "better-sqlite3": "^12.10.0",
     "chokidar": "^4.0.0",
     "kxta-core": "workspace:*",
     "re2": "^1.24.1",
@@ -73,5 +73,5 @@
     "tsup": "^8.3.0",
     "typescript": "^5.7.0"
   },
-  "rulesVersion": "2.0.0"
+  "rulesVersion": "2.1.0"
 }