@phren/cli 0.0.38 → 0.0.40

package/mcp/dist/cli/hooks.js

@@ -9,7 +9,7 @@ import { mergeConfig, } from "../shared/governance.js";
 import { buildIndex, detectProject, } from "../shared/index.js";
 import { isProjectHookEnabled } from "../project-config.js";
 import { checkConsolidationNeeded, } from "../shared/content.js";
-import { buildRobustFtsQuery, extractKeywordEntries, isFeatureEnabled, clampInt, errorMessage, loadSynonymMap, learnSynonym, STOP_WORDS, } from "../utils.js";
+import { buildRobustFtsQuery, extractKeywordEntries, isFeatureEnabled, clampInt, errorMessage, } from "../utils.js";
 import { getHooksEnabledPreference } from "../init/init.js";
 import { logger } from "../logger.js";
 import { isToolHookEnabled } from "../hooks.js";
@@ -37,65 +37,9 @@ import { getGitContext, trackSessionMetrics, } from "./hooks-session.js";
 import { approximateTokens } from "../shared/retrieval.js";
 import { resolveRuntimeProfile } from "../runtime-profile.js";
 import { handleTaskPromptLifecycle } from "../task/lifecycle.js";
-function synonymTermKnown(term, map) {
-    if (Object.prototype.hasOwnProperty.call(map, term))
-        return true;
-    for (const values of Object.values(map)) {
-        if (values.includes(term))
-            return true;
-    }
-    return false;
-}
-function termAppearsInText(term, text) {
-    const escaped = term.replace(/[.*+?^${}()|[\]\\]/g, "\\$&").replace(/\s+/g, "\\s+");
-    const pattern = new RegExp(`\\b${escaped}\\b`, "i");
-    return pattern.test(text);
-}
-function autoLearnQuerySynonyms(phrenPath, project, keywordEntries, rows) {
-    if (!project)
-        return;
-    const synonymMap = loadSynonymMap(project, phrenPath);
-    const knownTerms = new Set([
-        ...Object.keys(synonymMap),
-        ...Object.values(synonymMap).flat(),
-    ]);
-    const queryTerms = [...new Set(keywordEntries
-            .map((item) => item.trim().toLowerCase())
-            .filter((item) => item.length > 2 && !STOP_WORDS.has(item)))];
-    const unknownTerms = queryTerms.filter((term) => !synonymTermKnown(term, synonymMap));
-    if (unknownTerms.length === 0)
-        return;
-    const corpus = rows
-        .slice(0, 8)
-        .map((row) => row.content.slice(0, 6000))
-        .join("\n")
-        .toLowerCase();
-    if (!corpus.trim())
-        return;
-    const learned = [];
-    for (const unknown of unknownTerms.slice(0, 3)) {
-        const related = [...knownTerms]
-            .filter((candidate) => candidate.length > 2
-            && candidate !== unknown
-            && !STOP_WORDS.has(candidate)
-            && !queryTerms.includes(candidate)
-            && termAppearsInText(candidate, corpus))
-            .slice(0, 4);
-        if (related.length === 0)
-            continue;
-        try {
-            learnSynonym(phrenPath, project, unknown, related);
-            learned.push({ term: unknown, related });
-        }
-        catch (err) {
-            debugLog(`hook-prompt synonym-learn failed for "${unknown}": ${errorMessage(err)}`);
-        }
-    }
-    if (learned.length > 0) {
-        const details = learned.map((entry) => `${entry.term}->${entry.related.join(",")}`).join("; ");
-        debugLog(`hook-prompt learned synonyms project=${project} ${details}`);
-    }
-}
+// Auto-learn from prompts was removed — it learned conversational noise ("bro", "idk", typos)
+// as synonyms for high-frequency terms. Manual `phren config synonyms add` still works.
+// Future: finding-based co-occurrence mining (phren maintain command, not live hook).
 async function readStdin() {
     return new Promise((resolve, reject) => {
         const chunks = [];
@@ -195,7 +139,6 @@ export async function handleHookPrompt() {
         stage.searchMs = Date.now() - tSearch0;
         if (!rows || !rows.length)
             process.exit(0);
-        autoLearnQuerySynonyms(getPhrenPath(), detectedProject, keywordEntries, rows);
         const tTrust0 = Date.now();
         const policy = resolvedConfig.retentionPolicy;
         const memoryTtlDays = Number.parseInt(process.env.PHREN_MEMORY_TTL_DAYS || String(policy.ttlDays), 10);

package/mcp/dist/entrypoint.js

@@ -340,6 +340,7 @@ export async function runTopLevelCommand(argv) {
             applyStarterUpdate: initArgs.includes("--apply-starter-update"),
             dryRun: initArgs.includes("--dry-run"),
             yes: initArgs.includes("--yes") || initArgs.includes("-y"),
+            express: initArgs.includes("--express"),
             _walkthroughCloneUrl: cloneUrl,
         });
         return finish();

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-walkthrough.js

@@ -114,7 +114,7 @@ function detectRepoRootForStorage(phrenPath) {
     return detectProjectDir(process.cwd(), phrenPath);
 }
 // Interactive walkthrough for first-time init
-export async function runWalkthrough(phrenPath) {
+export async function runWalkthrough(phrenPath, options) {
     const prompts = await createWalkthroughPrompts();
     const style = await createWalkthroughStyle();
     const divider = style.header("━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━");
@@ -137,6 +137,42 @@ export async function runWalkthrough(phrenPath) {
     printSection("Welcome");
     log("Let's set up persistent memory for your AI agents.");
     log("Every option can be changed later.\n");
+    // Express mode: skip the entire walkthrough with recommended defaults
+    const useExpress = options?.express === true
+        || (options?.express !== false && await prompts.confirm("Use recommended settings? (global storage, MCP on, hooks on, auto tasks)", true));
+    if (useExpress) {
+        const expressResult = {
+            storageChoice: "global",
+            storagePath: path.resolve(homePath(".phren")),
+            machine: getMachineName(),
+            profile: "personal",
+            mcp: "on",
+            hooks: "on",
+            projectOwnershipDefault: "phren-managed",
+            findingsProactivity: "high",
+            taskProactivity: "high",
+            lowConfidenceThreshold: 0.7,
+            riskySections: ["Stale", "Conflicts"],
+            taskMode: "auto",
+            bootstrapCurrentProject: false,
+            ollamaEnabled: false,
+            autoCaptureEnabled: false,
+            semanticDedupEnabled: false,
+            semanticConflictEnabled: false,
+            findingSensitivity: "balanced",
+            domain: "software",
+        };
+        printSummary([
+            `Storage: global (${expressResult.storagePath})`,
+            `Machine: ${expressResult.machine}`,
+            "MCP: enabled",
+            "Hooks: enabled",
+            "Project ownership: phren-managed",
+            "Task mode: auto",
+            "Domain: software",
+        ]);
+        return expressResult;
+    }
     printSection("Storage Location");
     log("Where should phren store data?");
     const storageChoice = await prompts.select("Storage location", [

package/mcp/dist/init/init.js

@@ -7,7 +7,7 @@ import * as fs from "fs";
 import * as path from "path";
 import { execFileSync } from "child_process";
 import { getMachineName, persistMachineName } from "../machine-identity.js";
-import { atomicWriteText, debugLog, expandHomePath, hookConfigPath, writeRootManifest, } from "../shared.js";
+import { atomicWriteText, debugLog, expandHomePath, writeRootManifest, } from "../shared.js";
 import { isValidProjectName, errorMessage } from "../utils.js";
 import { logger } from "../logger.js";
 export { configureClaude, configureVSCode, configureCursorMcp, configureCopilotMcp, configureCodexMcp, logMcpTargetStatus, resetVSCodeProbeCache, patchJsonFile, } from "./config.js";
@@ -25,10 +25,11 @@ import { configureMcpTargets, configureHooksIfEnabled, applyOnboardingPreference
 import { runWalkthrough, createWalkthroughPrompts, createWalkthroughStyle } from "./init-walkthrough.js";
 import { getMcpEnabledPreference, getHooksEnabledPreference, writeInstallPreferences, readInstallPreferences, } from "./preferences.js";
 import { ensureGovernanceFiles, repairPreexistingInstall, runPostInitVerify, applyStarterTemplateUpdates, listTemplates, applyTemplate, ensureProjectScaffold, ensureLocalGitRepo, bootstrapFromExisting, updateMachinesYaml, detectProjectDir, isProjectTracked, } from "./setup.js";
-import { DEFAULT_PHREN_PATH, STARTER_DIR, VERSION, log, confirmPrompt } from "./shared.js";
+import { DEFAULT_PHREN_PATH, STARTER_DIR, VERSION, log } from "./shared.js";
 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, "-");
 }
@@ -147,8 +140,10 @@ export async function runInit(opts = {}) {
     }
     let hasExistingInstall = hasInstallMarkers(phrenPath);
     // Interactive walkthrough for first-time installs (skip with --yes or non-TTY)
-    if (!hasExistingInstall && !dryRun && !opts.yes && process.stdin.isTTY && process.stdout.isTTY) {
-        const answers = await runWalkthrough(phrenPath);
+    // --express bypasses the TTY check since it skips all interactive prompts
+    const isTTY = process.stdin.isTTY && process.stdout.isTTY;
+    if (!hasExistingInstall && !dryRun && !opts.yes && (isTTY || opts.express)) {
+        const answers = await runWalkthrough(phrenPath, { express: opts.express });
         opts._walkthroughStorageChoice = answers.storageChoice;
         opts._walkthroughStoragePath = answers.storagePath;
         opts._walkthroughStorageRepoRoot = answers.storageRepoRoot;
@@ -350,20 +345,6 @@ export async function runInit(opts = {}) {
         log(`  Default project ownership: ${ownershipDefault}`);
         log(`  Task mode: ${getWorkflowPolicy(phrenPath).taskMode}`);
         log(`  Git repo: ${existingGitRepo.detail}`);
-        // Confirmation prompt before writing config
-        if (!opts.yes) {
-            const settingsPath = hookConfigPath("claude");
-            const modifications = [];
-            modifications.push(`  ${settingsPath}  (update MCP server + hooks)`);
-            log(`\nWill modify:`);
-            for (const mod of modifications)
-                log(mod);
-            const confirmed = await confirmPrompt("\nProceed?");
-            if (!confirmed) {
-                log("Aborted.");
-                return;
-            }
-        }
         // Always reconfigure MCP and hooks (picks up new features on upgrade)
         configureMcpTargets(phrenPath, { mcpEnabled, hooksEnabled }, "Updated");
         configureHooksIfEnabled(phrenPath, hooksEnabled, "Updated");
@@ -546,17 +527,6 @@ export async function runInit(opts = {}) {
     if (repairedAssets.length > 0) {
         log(`  Recreated missing generated assets: ${repairedAssets.join(", ")}`);
     }
-    // Confirmation prompt before writing agent config
-    if (!opts.yes) {
-        const settingsPath = hookConfigPath("claude");
-        log(`\nWill modify:`);
-        log(`  ${settingsPath}  (add MCP server + hooks)`);
-        const confirmed = await confirmPrompt("\nProceed?");
-        if (!confirmed) {
-            log("Aborted.");
-            return;
-        }
-    }
     // Configure MCP for all detected AI coding tools and hooks
     configureMcpTargets(phrenPath, { mcpEnabled, hooksEnabled }, "Configured");
     configureHooksIfEnabled(phrenPath, hooksEnabled, "Configured");

package/mcp/dist/init/setup.js

@@ -891,8 +891,15 @@ export function ensureLocalGitRepo(phrenPath) {
             stdio: ["ignore", "pipe", "ignore"],
             timeout: EXEC_TIMEOUT_QUICK_MS,
         }).trim();
-        const resolvedTopLevel = path.resolve(topLevel);
-        const resolvedPhrenPath = path.resolve(phrenPath);
+        // Normalize both paths: resolve symlinks (macOS /var→/private/var) and
+        // on Windows resolve 8.3 short names (RUNNER~1→runneradmin) + case-insensitive
+        const realpath = process.platform === "win32" ? fs.realpathSync.native : fs.realpathSync;
+        let resolvedTopLevel = realpath(path.resolve(topLevel));
+        let resolvedPhrenPath = realpath(path.resolve(phrenPath));
+        if (process.platform === "win32") {
+            resolvedTopLevel = resolvedTopLevel.toLowerCase();
+            resolvedPhrenPath = resolvedPhrenPath.toLowerCase();
+        }
         if (resolvedTopLevel === resolvedPhrenPath) {
             // phrenPath IS the repo root — it has its own git repo
             return { ok: true, initialized: false, detail: "existing git repo" };

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": "0.0.40",
   "description": "Knowledge layer for AI agents. Phren learns and recalls.",
   "type": "module",
   "bin": {