@phren/cli 0.0.42 → 0.0.44

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

@@ -89,7 +89,7 @@ export function configureHooksIfEnabled(phrenPath, hooksEnabled, verb) {
         }
     }
     else {
-        log(`  Hooks are disabled by preference (run: npx phren hooks-mode on)`);
+        log(`  Hooks are disabled by preference (run: phren hooks-mode on)`);
     }
     // Install phren CLI wrapper at ~/.local/bin/phren so the bare command works
     const wrapperInstalled = installPhrenCliWrapper(phrenPath);

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

@@ -14,7 +14,7 @@ export async function runHooksMode(modeArg) {
     if (!normalizedArg || normalizedArg === "status") {
         const current = getHooksEnabledPreference(phrenPath);
         log(`Hooks mode: ${current ? "on (active)" : "off (disabled)"}`);
-        log(`Change mode: npx phren hooks-mode on|off`);
+        log(`Change mode: phren hooks-mode on|off`);
         return;
     }
     const mode = parseMcpMode(normalizedArg);

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

@@ -15,8 +15,8 @@ export async function runMcpMode(modeArg) {
         const hooks = getHooksEnabledPreference(phrenPath);
         log(`MCP mode: ${current ? "on (recommended)" : "off (hooks-only fallback)"}`);
         log(`Hooks mode: ${hooks ? "on (active)" : "off (disabled)"}`);
-        log(`Change mode: npx phren mcp-mode on|off`);
-        log(`Hooks toggle: npx phren hooks-mode on|off`);
+        log(`Change mode: phren mcp-mode on|off`);
+        log(`Hooks toggle: phren hooks-mode on|off`);
         return;
     }
     const mode = parseMcpMode(normalizedArg);

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

@@ -280,7 +280,7 @@ export async function runWalkthrough(phrenPath, options) {
     log("  phren-managed: Phren may mirror CLAUDE.md / AGENTS.md into the repo");
     log("  detached: Phren keeps its own docs but does not write into the repo");
     log("  repo-managed: keep the repo's existing CLAUDE/AGENTS files as canonical");
-    log("  Change later: npx phren config project-ownership <mode>");
+    log("  Change later: phren config project-ownership <mode>");
     const projectOwnershipDefault = await prompts.select("Default project ownership", [
         { value: "detached", name: "detached (default)" },
         { value: "phren-managed", name: "phren-managed" },
@@ -291,7 +291,7 @@ export async function runWalkthrough(phrenPath, options) {
     log("directly: search memory, manage tasks, save findings, etc.");
     log("  Recommended for: Claude Code, Cursor, Copilot CLI, Codex");
     log("  Alternative: hooks-only mode (read-only context injection, any agent)");
-    log("  Change later: npx phren mcp-mode on|off");
+    log("  Change later: phren mcp-mode on|off");
     const mcp = (await prompts.confirm("Enable MCP?", true)) ? "on" : "off";
     printSection("Hooks");
     log("Hooks run shell commands at session start, prompt submit, and session end.");
@@ -299,7 +299,7 @@ export async function runWalkthrough(phrenPath, options) {
     log("  - UserPromptSubmit: searches phren and injects relevant context");
     log("  - Stop: commits and pushes any new findings after each response");
     log("  What they touch: ~/.claude/settings.json (hooks section only)");
-    log("  Change later: npx phren hooks-mode on|off");
+    log("  Change later: phren hooks-mode on|off");
     const hooks = (await prompts.confirm("Enable hooks?", true)) ? "on" : "off";
     printSection("Semantic Search (Optional)");
     log("Phren can use a local embedding model for semantic (fuzzy) search via Ollama.");
@@ -347,7 +347,7 @@ export async function runWalkthrough(phrenPath, options) {
     let findingsProactivity = "high";
     if (autoCaptureEnabled) {
         log("  Findings capture level controls how eager phren is to save lessons automatically.");
-        log("  Change later: npx phren config proactivity.findings <high|medium|low>");
+        log("  Change later: phren config proactivity.findings <high|medium|low>");
         findingsProactivity = await prompts.select("Findings capture level", [
             { value: "high", name: "high (recommended)" },
             { value: "medium", name: "medium" },
@@ -363,7 +363,7 @@ export async function runWalkthrough(phrenPath, options) {
     log("  suggest: proposes tasks but waits for approval before writing");
     log("  manual: tasks are fully manual — you add them yourself");
     log("  off: never touch tasks automatically");
-    log("  Change later: npx phren config workflow set --taskMode=<mode>");
+    log("  Change later: phren config workflow set --taskMode=<mode>");
     const taskMode = await prompts.select("Task mode", [
         { value: "auto", name: "auto (recommended)" },
         { value: "suggest", name: "suggest" },
@@ -376,7 +376,7 @@ export async function runWalkthrough(phrenPath, options) {
         log("  high (recommended): captures tasks as they come up naturally");
         log("  medium: only when you explicitly mention a task");
         log("  low: minimal auto-capture");
-        log("  Change later: npx phren config proactivity.tasks <high|medium|low>");
+        log("  Change later: phren config proactivity.tasks <high|medium|low>");
         taskProactivity = await prompts.select("Task proactivity", [
             { value: "high", name: "high (recommended)" },
             { value: "medium", name: "medium" },
@@ -387,7 +387,7 @@ export async function runWalkthrough(phrenPath, options) {
     log("Choose how strict review gates should be for risky or low-confidence writes.");
     log("  lowConfidenceThreshold: confidence cutoff used to mark writes as risky");
     log("  riskySections: sections always treated as risky");
-    log("  Change later: npx phren config workflow set --lowConfidenceThreshold=0.7 --riskySections=Stale,Conflicts");
+    log("  Change later: phren config workflow set --lowConfidenceThreshold=0.7 --riskySections=Stale,Conflicts");
     const thresholdAnswer = await prompts.input("Low-confidence threshold [0.0-1.0]", "0.7");
     const lowConfidenceThreshold = parseLowConfidenceThreshold(thresholdAnswer, 0.7);
     const riskySectionsAnswer = await prompts.input("Risky sections [Review,Stale,Conflicts]", "Stale,Conflicts");
@@ -437,7 +437,7 @@ export async function runWalkthrough(phrenPath, options) {
     log("  conservative — decisions and pitfalls only");
     log("  balanced     — non-obvious patterns, decisions, pitfalls, bugs (recommended)");
     log("  aggressive   — everything worth remembering, err on the side of capturing");
-    log("  Change later: npx phren config finding-sensitivity <level>");
+    log("  Change later: phren config finding-sensitivity <level>");
     const findingSensitivity = await prompts.select("Finding sensitivity", [
         { value: "balanced", name: "balanced (recommended)" },
         { value: "conservative", name: "conservative" },
@@ -466,7 +466,7 @@ export async function runWalkthrough(phrenPath, options) {
         bootstrapCurrentProject = await prompts.confirm("Add this project to phren now?", true);
         if (!bootstrapCurrentProject) {
             bootstrapCurrentProject = false;
-            log(style.warning(`  Skipped. Later: cd ${detectedProject} && npx phren add`));
+            log(style.warning(`  Skipped. Later: cd ${detectedProject} && phren add`));
         }
         else {
             bootstrapOwnership = await prompts.select("Ownership for detected project", [

package/mcp/dist/init/init.js

@@ -260,7 +260,7 @@ export async function runInit(opts = {}) {
             shouldBootstrapCurrentProject = await prompts.confirm("Add this project to phren now?", true);
             if (!shouldBootstrapCurrentProject) {
                 shouldBootstrapCurrentProject = false;
-                log(style.warning(`  Skipped. Later: cd ${pendingBootstrap.path} && npx phren add`));
+                log(style.warning(`  Skipped. Later: cd ${pendingBootstrap.path} && phren add`));
             }
             else {
                 bootstrapOwnership = await prompts.select("Ownership for detected project", [
@@ -352,7 +352,7 @@ export async function runInit(opts = {}) {
         const previousVersion = prefs.installedVersion;
         if (isVersionNewer(VERSION, previousVersion)) {
             log(`\n  Starter template update available: v${previousVersion} -> v${VERSION}`);
-            log(`  Run \`npx phren init --apply-starter-update\` to refresh global/CLAUDE.md and global skills.`);
+            log(`  Run \`phren init --apply-starter-update\` to refresh global/CLAUDE.md and global skills.`);
         }
         if (opts.applyStarterUpdate) {
             const updated = applyStarterTemplateUpdates(phrenPath);
@@ -395,8 +395,8 @@ export async function runInit(opts = {}) {
         log(`\n\x1b[95m◆\x1b[0m phren updated successfully`);
         log(`\nNext steps:`);
         log(`  1. Start a new Claude session in your project directory — phren injects context automatically`);
-        log(`  2. Run \`npx phren doctor\` to verify everything is wired correctly`);
-        log(`  3. Change defaults anytime: \`npx phren config project-ownership\`, \`npx phren config workflow\`, \`npx phren config proactivity.findings\`, \`npx phren config proactivity.tasks\``);
+        log(`  2. Run \`phren doctor\` to verify everything is wired correctly`);
+        log(`  3. Change defaults anytime: \`phren config project-ownership\`, \`phren config workflow\`, \`phren config proactivity.findings\`, \`phren config proactivity.tasks\``);
         log(`  4. After your first week, run phren-discover to surface gaps in your project knowledge`);
         log(`  5. After working across projects, run phren-consolidate to find cross-project patterns`);
         log(``);
@@ -581,8 +581,8 @@ export async function runInit(opts = {}) {
     log(`\nNext steps:`);
     let step = 1;
     log(`  ${step++}. Start a new Claude session in your project directory — phren injects context automatically`);
-    log(`  ${step++}. Run \`npx phren doctor\` to verify everything is wired correctly`);
-    log(`  ${step++}. Change defaults anytime: \`npx phren config project-ownership\`, \`npx phren config workflow\`, \`npx phren config proactivity.findings\`, \`npx phren config proactivity.tasks\``);
+    log(`  ${step++}. Run \`phren doctor\` to verify everything is wired correctly`);
+    log(`  ${step++}. Change defaults anytime: \`phren config project-ownership\`, \`phren config workflow\`, \`phren config proactivity.findings\`, \`phren config proactivity.tasks\``);
     const gh = opts._walkthroughGithub;
     if (gh) {
         const remote = gh.username
@@ -607,9 +607,9 @@ export async function runInit(opts = {}) {
         log(`     git remote add origin git@github.com:YOUR_USERNAME/my-phren.git`);
         log(`     git push -u origin main`);
     }
-    log(`  ${step++}. Add more projects: cd ~/your-project && npx phren add`);
+    log(`  ${step++}. Add more projects: cd ~/your-project && phren add`);
     if (!mcpEnabled) {
-        log(`  ${step++}. Turn MCP on: npx phren mcp-mode on`);
+        log(`  ${step++}. Turn MCP on: phren mcp-mode on`);
     }
     log(`  ${step++}. After your first week, run phren-discover to surface gaps in your project knowledge`);
     log(`  ${step++}. After working across projects, run phren-consolidate to find cross-project patterns`);

package/mcp/dist/init/setup.js

@@ -278,6 +278,7 @@ export function repairPreexistingInstall(phrenPath) {
     const profileRepair = pruneLegacySampleProjectsFromProfiles(phrenPath);
     const preferredHome = resolvePreferredHomeDir(phrenPath);
     const createdSkillArtifacts = ensureGeneratedSkillArtifacts(phrenPath, preferredHome);
+    const repairedGlobalSymlink = repairGlobalClaudeSymlink(phrenPath);
     return {
         profileFilesUpdated: profileRepair.filesUpdated,
         removedLegacyProjects: profileRepair.removed,
@@ -287,8 +288,46 @@ export function repairPreexistingInstall(phrenPath) {
         createdRuntimeAssets,
         createdFeatureDefaults,
         createdSkillArtifacts,
+        repairedGlobalSymlink,
     };
 }
+/** Re-create ~/.claude/CLAUDE.md symlink if the source exists but the link is missing/broken. */
+function repairGlobalClaudeSymlink(phrenPath) {
+    const src = path.join(phrenPath, "global", "CLAUDE.md");
+    if (!fs.existsSync(src))
+        return false;
+    const dest = homePath(".claude", "CLAUDE.md");
+    try {
+        const stat = fs.lstatSync(dest);
+        if (stat.isSymbolicLink()) {
+            const target = path.resolve(path.dirname(dest), fs.readlinkSync(dest));
+            if (target === path.resolve(src))
+                return false; // already correct
+            // Stale symlink pointing elsewhere — managed by phren, safe to replace
+            if (target.includes(".phren"))
+                fs.unlinkSync(dest);
+            else
+                return false; // not ours, don't touch
+        }
+        else {
+            return false; // regular file exists, don't clobber
+        }
+    }
+    catch (err) {
+        if (err.code !== "ENOENT")
+            return false;
+    }
+    try {
+        fs.mkdirSync(path.dirname(dest), { recursive: true });
+        fs.symlinkSync(src, dest);
+        debugLog(`repaired global CLAUDE.md symlink: ${dest} -> ${src}`);
+        return true;
+    }
+    catch (err) {
+        debugLog(`failed to repair global CLAUDE.md symlink: ${errorMessage(err)}`);
+        return false;
+    }
+}
 function isExpectedVerifyFailure(phrenPath, check) {
     if (check.ok)
         return false;
@@ -1089,9 +1128,15 @@ export function updateMachinesYaml(phrenPath, machine, profile) {
  */
 export function detectProjectDir(dir, phrenPath) {
     const home = os.homedir();
+    const tmpRoot = path.resolve(os.tmpdir());
     const resolvedPhrenPath = path.resolve(phrenPath);
     let current = path.resolve(dir);
     while (true) {
+        // Never treat the shared OS temp root itself as a project. Tools may drop
+        // global instruction files there, which would otherwise hijack detection
+        // for arbitrary temp subdirectories.
+        if (current === tmpRoot)
+            return null;
         if (current === home || current === resolvedPhrenPath)
             return null;
         if (current.startsWith(resolvedPhrenPath + path.sep))
@@ -1306,7 +1351,7 @@ export function runPostInitVerify(phrenPath) {
         ok: true, // always pass — wrapper is optional (global install or npx work too)
         detail: cliWrapperOk
             ? `CLI wrapper exists: ${cliWrapperPath}`
-            : `CLI wrapper not found (optional — use 'npm i -g @phren/cli' or 'npx @phren/cli' instead)`,
+            : `CLI wrapper not found (optional — use 'npx @phren/cli' instead)`,
     });
     const ok = checks.every((c) => c.ok);
     return { ok, checks };

package/mcp/dist/init-fresh.js

@@ -197,8 +197,8 @@ export async function runFreshInstall(phrenPath, opts, params) {
     log(`\nNext steps:`);
     let step = 1;
     log(`  ${step++}. Start a new Claude session in your project directory — phren injects context automatically`);
-    log(`  ${step++}. Run \`npx phren doctor\` to verify everything is wired correctly`);
-    log(`  ${step++}. Change defaults anytime: \`npx phren config project-ownership\`, \`npx phren config workflow\`, \`npx phren config proactivity.findings\`, \`npx phren config proactivity.tasks\``);
+    log(`  ${step++}. Run \`phren doctor\` to verify everything is wired correctly`);
+    log(`  ${step++}. Change defaults anytime: \`phren config project-ownership\`, \`phren config workflow\`, \`phren config proactivity.findings\`, \`phren config proactivity.tasks\``);
     const gh = opts._walkthroughGithub;
     if (gh) {
         const remote = gh.username
@@ -223,9 +223,9 @@ export async function runFreshInstall(phrenPath, opts, params) {
         log(`     git remote add origin git@github.com:YOUR_USERNAME/my-phren.git`);
         log(`     git push -u origin main`);
     }
-    log(`  ${step++}. Add more projects: cd ~/your-project && npx phren add`);
+    log(`  ${step++}. Add more projects: cd ~/your-project && phren add`);
     if (!mcpEnabled) {
-        log(`  ${step++}. Turn MCP on: npx phren mcp-mode on`);
+        log(`  ${step++}. Turn MCP on: phren mcp-mode on`);
     }
     log(`  ${step++}. After your first week, run phren-discover to surface gaps in your project knowledge`);
     log(`  ${step++}. After working across projects, run phren-consolidate to find cross-project patterns`);

package/mcp/dist/init-hooks.js

@@ -21,6 +21,6 @@ export function configureHooksIfEnabled(phrenPath, hooksEnabled, verb) {
         }
     }
     else {
-        log(`  Hooks are disabled by preference (run: npx phren hooks-mode on)`);
+        log(`  Hooks are disabled by preference (run: phren hooks-mode on)`);
     }
 }

package/mcp/dist/init-modes.js

@@ -24,8 +24,8 @@ export async function runMcpMode(modeArg) {
         const hooks = getHooksEnabledPreference(phrenPath);
         log(`MCP mode: ${current ? "on (recommended)" : "off (hooks-only fallback)"}`);
         log(`Hooks mode: ${hooks ? "on (active)" : "off (disabled)"}`);
-        log(`Change mode: npx phren mcp-mode on|off`);
-        log(`Hooks toggle: npx phren hooks-mode on|off`);
+        log(`Change mode: phren mcp-mode on|off`);
+        log(`Hooks toggle: phren hooks-mode on|off`);
         return;
     }
     const mode = parseMcpMode(normalizedArg);
@@ -93,7 +93,7 @@ export async function runHooksMode(modeArg) {
     if (!normalizedArg || normalizedArg === "status") {
         const current = getHooksEnabledPreference(phrenPath);
         log(`Hooks mode: ${current ? "on (active)" : "off (disabled)"}`);
-        log(`Change mode: npx phren hooks-mode on|off`);
+        log(`Change mode: phren hooks-mode on|off`);
         return;
     }
     const mode = parseMcpMode(normalizedArg);

package/mcp/dist/init-update.js

@@ -53,7 +53,7 @@ export async function runExistingInstallUpdate(phrenPath, opts, params) {
     const previousVersion = prefs.installedVersion;
     if (isVersionNewer(VERSION, previousVersion)) {
         log(`\n  Starter template update available: v${previousVersion} -> v${VERSION}`);
-        log(`  Run \`npx phren init --apply-starter-update\` to refresh global/CLAUDE.md and global skills.`);
+        log(`  Run \`phren init --apply-starter-update\` to refresh global/CLAUDE.md and global skills.`);
     }
     if (opts.applyStarterUpdate) {
         const updated = applyStarterTemplateUpdates(phrenPath);
@@ -88,8 +88,8 @@ export async function runExistingInstallUpdate(phrenPath, opts, params) {
     log(`\n\x1b[95m◆\x1b[0m phren updated successfully`);
     log(`\nNext steps:`);
     log(`  1. Start a new Claude session in your project directory — phren injects context automatically`);
-    log(`  2. Run \`npx phren doctor\` to verify everything is wired correctly`);
-    log(`  3. Change defaults anytime: \`npx phren config project-ownership\`, \`npx phren config workflow\`, \`npx phren config proactivity.findings\`, \`npx phren config proactivity.tasks\``);
+    log(`  2. Run \`phren doctor\` to verify everything is wired correctly`);
+    log(`  3. Change defaults anytime: \`phren config project-ownership\`, \`phren config workflow\`, \`phren config proactivity.findings\`, \`phren config proactivity.tasks\``);
     log(`  4. After your first week, run phren-discover to surface gaps in your project knowledge`);
     log(`  5. After working across projects, run phren-consolidate to find cross-project patterns`);
     log(``);

package/mcp/dist/init-walkthrough.js

@@ -269,7 +269,7 @@ export async function runWalkthrough(phrenPath) {
     log("  phren-managed: Phren may mirror CLAUDE.md / AGENTS.md into the repo");
     log("  detached: Phren keeps its own docs but does not write into the repo");
     log("  repo-managed: keep the repo's existing CLAUDE/AGENTS files as canonical");
-    log("  Change later: npx phren config project-ownership <mode>");
+    log("  Change later: phren config project-ownership <mode>");
     const projectOwnershipDefault = await prompts.select("Default project ownership", [
         { value: "detached", name: "detached (default)" },
         { value: "phren-managed", name: "phren-managed" },
@@ -280,7 +280,7 @@ export async function runWalkthrough(phrenPath) {
     log("directly: search memory, manage tasks, save findings, etc.");
     log("  Recommended for: Claude Code, Cursor, Copilot CLI, Codex");
     log("  Alternative: hooks-only mode (read-only context injection, any agent)");
-    log("  Change later: npx phren mcp-mode on|off");
+    log("  Change later: phren mcp-mode on|off");
     const mcp = (await prompts.confirm("Enable MCP?", true)) ? "on" : "off";
     printSection("Hooks");
     log("Hooks run shell commands at session start, prompt submit, and session end.");
@@ -288,7 +288,7 @@ export async function runWalkthrough(phrenPath) {
     log("  - UserPromptSubmit: searches phren and injects relevant context");
     log("  - Stop: commits and pushes any new findings after each response");
     log("  What they touch: ~/.claude/settings.json (hooks section only)");
-    log("  Change later: npx phren hooks-mode on|off");
+    log("  Change later: phren hooks-mode on|off");
     const hooks = (await prompts.confirm("Enable hooks?", true)) ? "on" : "off";
     printSection("Semantic Search (Optional)");
     log("Phren can use a local embedding model for semantic (fuzzy) search via Ollama.");
@@ -336,7 +336,7 @@ export async function runWalkthrough(phrenPath) {
     let findingsProactivity = "high";
     if (autoCaptureEnabled) {
         log("  Findings capture level controls how eager phren is to save lessons automatically.");
-        log("  Change later: npx phren config proactivity.findings <high|medium|low>");
+        log("  Change later: phren config proactivity.findings <high|medium|low>");
         findingsProactivity = await prompts.select("Findings capture level", [
             { value: "high", name: "high (recommended)" },
             { value: "medium", name: "medium" },
@@ -352,7 +352,7 @@ export async function runWalkthrough(phrenPath) {
     log("  suggest: proposes tasks but waits for approval before writing");
     log("  manual: tasks are fully manual — you add them yourself");
     log("  off: never touch tasks automatically");
-    log("  Change later: npx phren config workflow set --taskMode=<mode>");
+    log("  Change later: phren config workflow set --taskMode=<mode>");
     const taskMode = await prompts.select("Task mode", [
         { value: "auto", name: "auto (recommended)" },
         { value: "suggest", name: "suggest" },
@@ -365,7 +365,7 @@ export async function runWalkthrough(phrenPath) {
         log("  high (recommended): captures tasks as they come up naturally");
         log("  medium: only when you explicitly mention a task");
         log("  low: minimal auto-capture");
-        log("  Change later: npx phren config proactivity.tasks <high|medium|low>");
+        log("  Change later: phren config proactivity.tasks <high|medium|low>");
         taskProactivity = await prompts.select("Task proactivity", [
             { value: "high", name: "high (recommended)" },
             { value: "medium", name: "medium" },
@@ -376,7 +376,7 @@ export async function runWalkthrough(phrenPath) {
     log("Choose how strict review gates should be for risky or low-confidence writes.");
     log("  lowConfidenceThreshold: confidence cutoff used to mark writes as risky");
     log("  riskySections: sections always treated as risky");
-    log("  Change later: npx phren config workflow set --lowConfidenceThreshold=0.7 --riskySections=Stale,Conflicts");
+    log("  Change later: phren config workflow set --lowConfidenceThreshold=0.7 --riskySections=Stale,Conflicts");
     const thresholdAnswer = await prompts.input("Low-confidence threshold [0.0-1.0]", "0.7");
     const lowConfidenceThreshold = parseLowConfidenceThreshold(thresholdAnswer, 0.7);
     const riskySectionsAnswer = await prompts.input("Risky sections [Review,Stale,Conflicts]", "Stale,Conflicts");
@@ -426,7 +426,7 @@ export async function runWalkthrough(phrenPath) {
     log("  conservative — decisions and pitfalls only");
     log("  balanced     — non-obvious patterns, decisions, pitfalls, bugs (recommended)");
     log("  aggressive   — everything worth remembering, err on the side of capturing");
-    log("  Change later: npx phren config finding-sensitivity <level>");
+    log("  Change later: phren config finding-sensitivity <level>");
     const findingSensitivity = await prompts.select("Finding sensitivity", [
         { value: "balanced", name: "balanced (recommended)" },
         { value: "conservative", name: "conservative" },
@@ -455,7 +455,7 @@ export async function runWalkthrough(phrenPath) {
         bootstrapCurrentProject = await prompts.confirm("Add this project to phren now?", true);
         if (!bootstrapCurrentProject) {
             bootstrapCurrentProject = false;
-            log(style.warning(`  Skipped. Later: cd ${detectedProject} && npx phren add`));
+            log(style.warning(`  Skipped. Later: cd ${detectedProject} && phren add`));
         }
         else {
             bootstrapOwnership = await prompts.select("Ownership for detected project", [

package/mcp/dist/link/doctor.js

@@ -409,7 +409,7 @@ export async function runDoctor(phrenPath, fix = false, checkData = false) {
         ok: phrenCliActive,
         detail: phrenCliActive
             ? "phren CLI wrapper active via ~/.local/bin/phren"
-            : "phren CLI wrapper missing — run init to install, or npm i -g @phren/cli",
+            : "phren CLI wrapper missing — run 'npx @phren/cli init' to install",
     });
     if (fix) {
         const repaired = repairPreexistingInstall(phrenPath);

package/mcp/dist/link/link.js

@@ -76,7 +76,7 @@ function maybeOfferStarterTemplateUpdate(phrenPath) {
         const prefs = JSON.parse(fs.readFileSync(prefsPath, "utf8"));
         if (isVersionNewer(current, prefs.installedVersion)) {
             log(`  Starter template update available: v${prefs.installedVersion} -> v${current}`);
-            log(`  Run \`npx phren init --apply-starter-update\` to refresh global/CLAUDE.md and global skills.`);
+            log(`  Run \`phren init --apply-starter-update\` to refresh global/CLAUDE.md and global skills.`);
         }
     }
     catch (err) {

package/mcp/dist/phren-paths.js

@@ -209,7 +209,7 @@ export function findPhrenPathWithArg(arg) {
     const existing = findPhrenPath();
     if (existing)
         return existing;
-    throw new Error(`${PhrenError.NOT_FOUND}: phren root not found. Run 'npx phren init'.`);
+    throw new Error(`${PhrenError.NOT_FOUND}: phren root not found. Run 'phren init'.`);
 }
 export function isProjectLocalMode(phrenPath) {
     try {
@@ -513,7 +513,7 @@ export function getPhrenPath() {
     if (!lazyPhrenPath) {
         const existing = findPhrenPath();
         if (!existing)
-            throw new Error(`${PhrenError.NOT_FOUND}: phren root not found. Run 'npx phren init'.`);
+            throw new Error(`${PhrenError.NOT_FOUND}: phren root not found. Run 'phren init'.`);
         lazyPhrenPath = existing;
     }
     return lazyPhrenPath;

package/mcp/dist/profile-store.js

@@ -45,7 +45,7 @@ export function resolveActiveProfile(phrenPath, requestedProfile) {
 export function listMachines(phrenPath) {
     const machinesPath = path.join(phrenPath, "machines.yaml");
     if (!fs.existsSync(machinesPath))
-        return phrenErr(`machines.yaml not found. Run 'npx phren init' to set up your phren.`, PhrenError.FILE_NOT_FOUND);
+        return phrenErr(`machines.yaml not found. Run 'phren init' to set up your phren.`, PhrenError.FILE_NOT_FOUND);
     try {
         const raw = fs.readFileSync(machinesPath, "utf8");
         const parsed = yaml.load(raw, { schema: yaml.CORE_SCHEMA });
@@ -205,7 +205,7 @@ export function getActiveProfileDefaults(phrenPath, profile) {
 export function listProfiles(phrenPath) {
     const profilesDir = path.join(phrenPath, "profiles");
     if (!fs.existsSync(profilesDir))
-        return phrenErr(`No profiles/ directory found. Run 'npx phren init' to set up your phren.`, PhrenError.FILE_NOT_FOUND);
+        return phrenErr(`No profiles/ directory found. Run 'phren init' to set up your phren.`, PhrenError.FILE_NOT_FOUND);
     const files = fs.readdirSync(profilesDir).filter((file) => file.endsWith(".yaml")).sort();
     const profiles = [];
     for (const file of files) {

package/mcp/dist/shared/retrieval.js

@@ -627,9 +627,15 @@ export function rankResults(rows, intent, gitCtx, detectedProject, phrenPathLoca
             }
             return false;
         });
-        const canonicalRows = queryDocRows(db, "SELECT project, filename, type, content, path FROM docs WHERE project = ? AND type = 'canonical' LIMIT 1", [detectedProject]);
-        if (canonicalRows)
-            ranked = [...canonicalRows, ...ranked];
+        // Always-inject: truths for detected project are prepended regardless of search
+        // relevance. Dedup against rows already in the result set.
+        const canonicalRows = queryDocRows(db, "SELECT project, filename, type, content, path FROM docs WHERE project = ? AND type = 'canonical'", [detectedProject]);
+        if (canonicalRows) {
+            const existingPaths = new Set(ranked.map((r) => r.path));
+            const newCanonicals = canonicalRows.filter((r) => !existingPaths.has(r.path));
+            if (newCanonicals.length > 0)
+                ranked = [...newCanonicals, ...ranked];
+        }
     }
     const entityBoost = query ? getFragmentBoostDocs(db, query) : new Set();
     const entityBoostPaths = new Set();

package/mcp/dist/status.js

@@ -53,7 +53,7 @@ function hasCommandHook(value) {
 export async function runStatus() {
     const phrenPath = findPhrenPath();
     if (!phrenPath) {
-        console.log(`${RED}phren not found${RESET}. Run ${CYAN}npx phren init${RESET} to set up.`);
+        console.log(`${RED}phren not found${RESET}. Run ${CYAN}npx @phren/cli init${RESET} to set up.`);
         process.exit(1);
     }
     const cwd = process.cwd();

package/mcp/dist/store-registry.js

@@ -165,6 +165,19 @@ export function removeStoreFromRegistry(phrenPath, name) {
         return entry;
     });
 }
+/** Update the projects[] claim list for a store. Uses file locking. */
+export function updateStoreProjects(phrenPath, storeName, projects) {
+    withFileLock(storesFilePath(phrenPath), () => {
+        const registry = readStoreRegistry(phrenPath);
+        if (!registry)
+            throw new Error(`${PhrenError.FILE_NOT_FOUND}: No stores.yaml found`);
+        const store = registry.stores.find((s) => s.name === storeName);
+        if (!store)
+            throw new Error(`${PhrenError.NOT_FOUND}: Store "${storeName}" not found`);
+        store.projects = projects.length > 0 ? projects : undefined;
+        writeStoreRegistry(phrenPath, registry);
+    });
+}
 // ── Validation ───────────────────────────────────────────────────────────────
 function validateRegistry(registry) {
     if (registry.version !== 1)
@@ -247,8 +260,9 @@ function parseFederationPathsEnv(localPhrenPath) {
     const raw = process.env.PHREN_FEDERATION_PATHS ?? "";
     if (!raw.trim())
         return [];
+    // Use path.delimiter (';' on Windows, ':' on Unix) so Windows drive letters aren't split
     return raw
-        .split(":")
+        .split(path.delimiter)
         .map((p) => p.trim())
         .filter((p) => p.length > 0)
         .map((p) => path.resolve(expandHomePath(p)))