@phren/cli 0.0.38 → 0.0.39

package/mcp/dist/governance/locks.js

@@ -24,10 +24,33 @@ function acquireFileLock(lockPath) {
             try {
                 const stat = fs.statSync(lockPath);
                 if (Date.now() - stat.mtimeMs > staleThreshold) {
-                    // Lock file is older than stale threshold — delete unconditionally.
-                    // This handles zombie processes, crashed hooks, and any case where
-                    // the owning process failed to clean up.
-                    fs.unlinkSync(lockPath);
+                    // Lock mtime exceeds stale threshold — but only delete if the
+                    // owning process is dead.  Legitimate long operations (e.g. index
+                    // rebuilds) can hold locks beyond the threshold.
+                    let ownerAlive = false;
+                    try {
+                        const content = fs.readFileSync(lockPath, "utf-8");
+                        const pid = Number.parseInt(content.split("\n")[0], 10);
+                        if (pid > 0 && Number.isFinite(pid)) {
+                            try {
+                                process.kill(pid, 0); // signal 0: liveness check, no actual signal sent
+                                ownerAlive = true;
+                            }
+                            catch {
+                                // process.kill throws if PID doesn't exist → owner is dead
+                            }
+                        }
+                        // pid <= 0 or NaN → treat as stale (unparseable / corrupt lock)
+                    }
+                    catch {
+                        // Can't read lock file (deleted between stat and read) → retry
+                    }
+                    if (!ownerAlive) {
+                        try {
+                            fs.unlinkSync(lockPath);
+                        }
+                        catch { /* already gone */ }
+                    }
                     continue;
                 }
             }

package/mcp/dist/init/init-hooks-mode.js

@@ -6,8 +6,7 @@ import { errorMessage } from "../utils.js";
 import { configureAllHooks } from "../hooks.js";
 import { configureClaude } from "./config.js";
 import { getMcpEnabledPreference, getHooksEnabledPreference, setHooksEnabledPreference, } from "./preferences.js";
-import { DEFAULT_PHREN_PATH, log } from "./shared.js";
-import { parseMcpMode } from "./init.js";
+import { DEFAULT_PHREN_PATH, log, parseMcpMode } from "./shared.js";
 export async function runHooksMode(modeArg) {
     const phrenPath = findPhrenPath() || (process.env.PHREN_PATH) || DEFAULT_PHREN_PATH;
     const manifest = readRootManifest(phrenPath);

package/mcp/dist/init/init-mcp-mode.js

@@ -5,8 +5,7 @@ import { debugLog, findPhrenPath, readRootManifest } from "../shared.js";
 import { errorMessage } from "../utils.js";
 import { configureClaude, configureVSCode, configureCursorMcp, configureCopilotMcp, configureCodexMcp, } from "./config.js";
 import { getMcpEnabledPreference, getHooksEnabledPreference, setMcpEnabledPreference, } from "./preferences.js";
-import { DEFAULT_PHREN_PATH, log } from "./shared.js";
-import { parseMcpMode } from "./init.js";
+import { DEFAULT_PHREN_PATH, log, parseMcpMode } from "./shared.js";
 export async function runMcpMode(modeArg) {
     const phrenPath = findPhrenPath() || (process.env.PHREN_PATH) || DEFAULT_PHREN_PATH;
     const manifest = readRootManifest(phrenPath);

package/mcp/dist/init/init.js

@@ -29,6 +29,7 @@ import { DEFAULT_PHREN_PATH, STARTER_DIR, VERSION, log, confirmPrompt } from "./
 import { PROJECT_OWNERSHIP_MODES, getProjectOwnershipDefault, } from "../project-config.js";
 import { getWorkflowPolicy } from "../shared/governance.js";
 import { addProjectToProfile } from "../profile-store.js";
+export { parseMcpMode } from "./shared.js";
 function parseVersion(version) {
     const match = version.trim().match(/^(\d+)\.(\d+)\.(\d+)(?:-(.+))?/);
     if (!match)
@@ -63,14 +64,6 @@ export function isVersionNewer(current, previous) {
         return true;
     return c.pre > p.pre;
 }
-export function parseMcpMode(raw) {
-    if (!raw)
-        return undefined;
-    const normalized = raw.trim().toLowerCase();
-    if (normalized === "on" || normalized === "off")
-        return normalized;
-    return undefined;
-}
 function normalizedBootstrapProjectName(projectPath) {
     return path.basename(projectPath).toLowerCase().replace(/[^a-z0-9_-]/g, "-");
 }

package/mcp/dist/init/shared.js

@@ -67,6 +67,14 @@ export function nearestWritableTarget(filePath) {
         return false;
     }
 }
+export function parseMcpMode(raw) {
+    if (!raw)
+        return undefined;
+    const normalized = raw.trim().toLowerCase();
+    if (normalized === "on" || normalized === "off")
+        return normalized;
+    return undefined;
+}
 export async function confirmPrompt(message) {
     if (process.env.CI === "true" || !process.stdin.isTTY)
         return true;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@phren/cli",
-  "version": "0.0.38",
+  "version": "0.0.39",
   "description": "Knowledge layer for AI agents. Phren learns and recalls.",
   "type": "module",
   "bin": {