@phren/cli 0.0.36 → 0.0.38

package/mcp/dist/init/setup.js

@@ -884,15 +884,25 @@ export function ensureProjectScaffold(projectDir, projectName, domain = "softwar
     }
 }
 export function ensureLocalGitRepo(phrenPath) {
+    // Check if phrenPath already has its own git repo (not just being inside a parent)
     try {
-        execFileSync("git", ["-C", phrenPath, "rev-parse", "--is-inside-work-tree"], {
-            stdio: ["ignore", "ignore", "ignore"],
+        const topLevel = execFileSync("git", ["-C", phrenPath, "rev-parse", "--show-toplevel"], {
+            encoding: "utf8",
+            stdio: ["ignore", "pipe", "ignore"],
             timeout: EXEC_TIMEOUT_QUICK_MS,
-        });
-        return { ok: true, initialized: false, detail: "existing git repo" };
+        }).trim();
+        const resolvedTopLevel = path.resolve(topLevel);
+        const resolvedPhrenPath = path.resolve(phrenPath);
+        if (resolvedTopLevel === resolvedPhrenPath) {
+            // phrenPath IS the repo root — it has its own git repo
+            return { ok: true, initialized: false, detail: "existing git repo" };
+        }
+        // phrenPath is inside a parent repo — skip nested init
+        logger.warn("init", `Skipping git init: ${resolvedPhrenPath} is inside existing repo ${resolvedTopLevel}`);
+        return { ok: true, initialized: false, detail: `skipped: inside existing repo ${resolvedTopLevel}` };
     }
     catch {
-        // Fall through to initialization below.
+        // Not inside any git repo — fall through to initialization below.
     }
     try {
         try {

package/mcp/dist/init-uninstall.js

@@ -170,8 +170,17 @@ function filterAgentHooks(filePath, commandField) {
         return true;
     }
     catch (err) {
-        debugLog(`filterAgentHooks: failed for ${filePath}: ${errorMessage(err)}`);
-        return false;
+        // JSON parse or other failure — back up the corrupted file so uninstall can proceed
+        const bakPath = filePath + ".bak";
+        try {
+            fs.renameSync(filePath, bakPath);
+            log(`  Warning: corrupted hook config backed up to ${bakPath} (${errorMessage(err)})`);
+        }
+        catch (bakErr) {
+            debugLog(`filterAgentHooks: backup failed for ${filePath}: ${errorMessage(bakErr)}`);
+            log(`  Warning: could not process hook config ${filePath}: ${errorMessage(err)}`);
+        }
+        return true;
     }
 }
 async function promptUninstallConfirm(phrenPath) {

package/mcp/dist/phren-paths.js

@@ -35,7 +35,16 @@ export function atomicWriteText(filePath, content) {
     fs.mkdirSync(path.dirname(filePath), { recursive: true });
     const tmpPath = `${filePath}.tmp-${crypto.randomUUID()}`;
     fs.writeFileSync(tmpPath, content);
-    fs.renameSync(tmpPath, filePath);
+    try {
+        fs.renameSync(tmpPath, filePath);
+    }
+    catch (err) {
+        try {
+            fs.unlinkSync(tmpPath);
+        }
+        catch { }
+        throw err;
+    }
 }
 function isInstallMode(value) {
     return value === "shared" || value === "project-local";
@@ -51,8 +60,16 @@ function normalizeManifest(raw) {
     const syncMode = raw.syncMode;
     if (version !== 1 || !isInstallMode(installMode) || !isSyncMode(syncMode))
         return null;
-    const workspaceRoot = typeof raw.workspaceRoot === "string" && raw.workspaceRoot.trim()
-        ? path.resolve(expandHomePath(raw.workspaceRoot))
+    let workspaceRootRaw = typeof raw.workspaceRoot === "string" && raw.workspaceRoot.trim()
+        ? raw.workspaceRoot.trim()
+        : undefined;
+    // Cross-platform path normalization: convert Windows backslashes to forward slashes
+    // when reading on a non-Windows platform (e.g. manifest created on Windows, read on Linux).
+    if (workspaceRootRaw && process.platform !== "win32") {
+        workspaceRootRaw = workspaceRootRaw.replace(/\\/g, "/");
+    }
+    const workspaceRoot = workspaceRootRaw
+        ? path.resolve(expandHomePath(workspaceRootRaw))
         : undefined;
     const primaryProject = typeof raw.primaryProject === "string" && raw.primaryProject.trim()
         ? raw.primaryProject.trim()

package/mcp/dist/shared/index.js

@@ -22,7 +22,13 @@ export { buildSourceDocKey, decodeFiniteNumber, decodeStringRow, extractSnippet,
 // ── Async embedding queue ───────────────────────────────────────────────────
 const _embQueue = new Map();
 let _embTimer = null;
+const MAX_EMB_QUEUE = 500;
 function scheduleEmbedding(phrenPath, docPath, content) {
+    if (_embQueue.size >= MAX_EMB_QUEUE) {
+        const oldest = _embQueue.keys().next().value;
+        if (oldest !== undefined)
+            _embQueue.delete(oldest);
+    }
     _embQueue.set(docPath, { phrenPath, content });
     if (_embTimer)
         clearTimeout(_embTimer);
@@ -63,6 +69,7 @@ async function _drainEmbQueue() {
             }
             catch (err) {
                 logger.debug("embeddingQueue embedText", errorMessage(err));
+                _embQueue.clear();
             }
         }
         try {
@@ -70,6 +77,7 @@ async function _drainEmbQueue() {
         }
         catch (err) {
             logger.debug("embeddingQueue cacheFlush", errorMessage(err));
+            _embQueue.clear();
         }
     }
 }

package/mcp/dist/task/lifecycle.js

@@ -302,7 +302,7 @@ export function finalizeTaskSession(args) {
     if (!state || state.mode !== "auto")
         return;
     const match = state.stableId ? `bid:${state.stableId}` : state.item;
-    if (args.status === "saved-local" || args.status === "saved-pushed") {
+    if (args.status === "saved-local" || args.status === "saved-pushed" || args.status === "no-upstream") {
         const completed = completeTask(args.phrenPath, state.project, match);
         if (!completed.ok) {
             debugLog(`task lifecycle complete ${state.project}: ${completed.error}`);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@phren/cli",
-  "version": "0.0.36",
+  "version": "0.0.38",
   "description": "Knowledge layer for AI agents. Phren learns and recalls.",
   "type": "module",
   "bin": {
@@ -51,6 +51,7 @@
     "bench:retrieval": "tsx scripts/bench-retrieval-modes.ts",
     "bench:retrieval:synthetic": "tsx scripts/bench-retrieval-synthetic.ts",
     "preuninstall": "node scripts/preuninstall.mjs",
+    "install-hooks": "cp scripts/pre-commit .git/hooks/pre-commit && chmod +x .git/hooks/pre-commit",
     "prepublishOnly": "npm run build && npm test"
   },
   "engines": {