@phren/cli 0.0.26 → 0.0.28

package/mcp/dist/entrypoint.js

@@ -325,6 +325,7 @@ export async function runTopLevelCommand(argv) {
             console.error(`Invalid --task-proactivity value "${taskArg}". Use one of: high, medium, low.`);
             return finish(1);
         }
+        const cloneUrl = getOptionValue(initArgs, "--clone-url");
         await runInit({
             mode: modeArg,
             machine: machineIdx !== -1 ? initArgs[machineIdx + 1] : undefined,
@@ -338,6 +339,7 @@ export async function runTopLevelCommand(argv) {
             applyStarterUpdate: initArgs.includes("--apply-starter-update"),
             dryRun: initArgs.includes("--dry-run"),
             yes: initArgs.includes("--yes") || initArgs.includes("-y"),
+            _walkthroughCloneUrl: cloneUrl,
         });
         return finish();
     }

package/mcp/dist/init.js

@@ -85,19 +85,16 @@ function runSyncCommand(command, args) {
     }
 }
 function shouldUninstallCurrentGlobalPackage() {
-    const entryScript = process.argv[1];
-    if (!entryScript)
-        return false;
+    // Always attempt to remove the global package if it exists, regardless of
+    // whether the uninstaller was invoked from the global install or a local repo.
     const npmRootResult = runSyncCommand(getNpmCommand(), ["root", "-g"]);
     if (!npmRootResult.ok)
         return false;
     const npmRoot = npmRootResult.stdout.trim();
     if (!npmRoot)
         return false;
-    const resolvedEntryScript = path.resolve(entryScript);
-    const resolvedGlobalPackageRoot = path.resolve(path.join(npmRoot, PHREN_NPM_PACKAGE_NAME));
-    return resolvedEntryScript === resolvedGlobalPackageRoot
-        || resolvedEntryScript.startsWith(`${resolvedGlobalPackageRoot}${path.sep}`);
+    const globalPkgPath = path.join(npmRoot, PHREN_NPM_PACKAGE_NAME);
+    return fs.existsSync(globalPkgPath);
 }
 function uninstallCurrentGlobalPackage() {
     const result = runSyncCommand(getNpmCommand(), ["uninstall", "-g", PHREN_NPM_PACKAGE_NAME]);
@@ -1682,8 +1679,29 @@ function sweepSkillSymlinks(phrenPath) {
                     log(`  Removed skill symlink: ${fullPath}`);
                 }
             }
+            catch {
+                // Broken symlink (target no longer exists) — clean it up
+                try {
+                    fs.unlinkSync(fullPath);
+                    log(`  Removed broken skill symlink: ${fullPath}`);
+                }
+                catch (err2) {
+                    debugLog(`sweepSkillSymlinks: could not remove broken symlink ${fullPath}: ${errorMessage(err2)}`);
+                }
+            }
+        }
+        // Remove phren-generated manifest files from the skills parent directory
+        const parentDir = path.dirname(dir);
+        for (const manifestFile of ["skill-manifest.json", "skill-commands.json"]) {
+            const manifestPath = path.join(parentDir, manifestFile);
+            try {
+                if (fs.existsSync(manifestPath)) {
+                    fs.unlinkSync(manifestPath);
+                    log(`  Removed ${manifestFile} (${manifestPath})`);
+                }
+            }
             catch (err) {
-                debugLog(`sweepSkillSymlinks: could not check/remove ${fullPath}: ${errorMessage(err)}`);
+                debugLog(`sweepSkillSymlinks: could not remove ${manifestPath}: ${errorMessage(err)}`);
             }
         }
     }
@@ -2008,6 +2026,33 @@ export async function runUninstall(opts = {}) {
     if (shouldRemoveGlobalPackage) {
         uninstallCurrentGlobalPackage();
     }
+    // Remove VS Code extension if installed
+    try {
+        const codeResult = execFileSync("code", ["--list-extensions"], {
+            encoding: "utf8",
+            stdio: ["ignore", "pipe", "ignore"],
+            timeout: 10_000,
+        });
+        const phrenExts = codeResult.split("\n").filter((ext) => ext.toLowerCase().includes("phren"));
+        for (const ext of phrenExts) {
+            const trimmed = ext.trim();
+            if (!trimmed)
+                continue;
+            try {
+                execFileSync("code", ["--uninstall-extension", trimmed], {
+                    stdio: ["ignore", "pipe", "ignore"],
+                    timeout: 15_000,
+                });
+                log(`  Removed VS Code extension (${trimmed})`);
+            }
+            catch (err) {
+                debugLog(`uninstall: VS Code extension removal failed for ${trimmed}: ${errorMessage(err)}`);
+            }
+        }
+    }
+    catch {
+        // code CLI not available — skip
+    }
     log(`\nPhren config, hooks, and installed data removed.`);
     log(`Restart your agent(s) to apply changes.\n`);
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@phren/cli",
-  "version": "0.0.26",
+  "version": "0.0.28",
   "description": "Knowledge layer for AI agents. Phren learns and recalls.",
   "type": "module",
   "bin": {
@@ -10,7 +10,8 @@
     "mcp/dist",
     "icon.svg",
     "starter",
-    "skills"
+    "skills",
+    "scripts/preuninstall.mjs"
   ],
   "dependencies": {
     "@modelcontextprotocol/sdk": "^1.27.1",
@@ -19,7 +20,7 @@
     "glob": "^13.0.6",
     "graphology": "^0.26.0",
     "graphology-layout-forceatlas2": "^0.10.1",
-    "inquirer": "^12.10.0",
+    "inquirer": "^13.3.2",
     "js-yaml": "^4.1.1",
     "sigma": "^3.0.2",
     "sql.js-fts5": "^1.4.0",
@@ -28,14 +29,14 @@
   "devDependencies": {
     "@playwright/test": "^1.58.2",
     "@types/js-yaml": "^4.0.9",
-    "@types/node": "^25.3.5",
-    "@typescript-eslint/eslint-plugin": "^8.56.1",
-    "@typescript-eslint/parser": "^8.56.1",
-    "@vitest/coverage-v8": "^4.0.18",
-    "eslint": "^10.0.3",
+    "@types/node": "^25.5.0",
+    "@typescript-eslint/eslint-plugin": "^8.57.1",
+    "@typescript-eslint/parser": "^8.57.1",
+    "@vitest/coverage-v8": "^4.1.0",
+    "eslint": "^10.1.0",
     "tsx": "^4.21.0",
     "typescript": "^5.9.3",
-    "vitest": "^4.0.18"
+    "vitest": "^4.1.0"
   },
   "scripts": {
     "build": "node scripts/build.mjs",
@@ -49,6 +50,7 @@
     "bench": "tsx mcp/bench/locomo-runner.ts --sessions 3",
     "bench:retrieval": "tsx scripts/bench-retrieval-modes.ts",
     "bench:retrieval:synthetic": "tsx scripts/bench-retrieval-synthetic.ts",
+    "preuninstall": "node scripts/preuninstall.mjs",
     "prepublishOnly": "npm run build && npm test"
   },
   "engines": {
@@ -67,5 +69,9 @@
     "type": "git",
     "url": "git+https://github.com/alaarab/phren.git"
   },
-  "homepage": "https://github.com/alaarab/phren#readme"
+  "homepage": "https://github.com/alaarab/phren#readme",
+  "overrides": {
+    "flatted": "^3.4.2",
+    "undici": "^7.10.0"
+  }
 }

package/scripts/preuninstall.mjs

@@ -0,0 +1,108 @@
+#!/usr/bin/env node
+
+/**
+ * npm preuninstall hook — clean up hooks and MCP server entries from agent
+ * config files so they don't become orphaned when the package is removed
+ * via `npm uninstall -g @phren/cli` (bypassing `phren uninstall`).
+ *
+ * Only removes config/hooks — does NOT touch ~/.phren data.
+ */
+
+import fs from "node:fs";
+import path from "node:path";
+import { fileURLToPath } from "node:url";
+
+const home = process.env.HOME || process.env.USERPROFILE || "/tmp";
+const homePath = (...parts) => path.join(home, ...parts);
+
+/** Read JSON, apply mutator, write back. */
+function patchJson(filePath, mutator) {
+  if (!fs.existsSync(filePath)) return;
+  try {
+    const data = JSON.parse(fs.readFileSync(filePath, "utf8"));
+    mutator(data);
+    fs.writeFileSync(filePath, JSON.stringify(data, null, 2) + "\n");
+  } catch {
+    // best-effort — don't fail the uninstall
+  }
+}
+
+/** Check if a hook command string belongs to phren. */
+function isPhrenCommand(cmd) {
+  return (
+    cmd.includes("@phren/cli") ||
+    cmd.includes("phren/cli") ||
+    /\bhook-(prompt|stop|session-start|tool|context)\b/.test(cmd)
+  );
+}
+
+// ── Claude Code settings.json: remove hooks + MCP server ──
+const claudeSettings = homePath(".claude", "settings.json");
+patchJson(claudeSettings, (data) => {
+  // Remove MCP server
+  if (data.mcpServers?.phren) delete data.mcpServers.phren;
+
+  // Remove phren hooks
+  if (data.hooks && typeof data.hooks === "object") {
+    for (const event of ["UserPromptSubmit", "Stop", "SessionStart", "PostToolUse"]) {
+      const entries = data.hooks[event];
+      if (!Array.isArray(entries)) continue;
+      data.hooks[event] = entries.filter(
+        (entry) => !entry.hooks?.some((h) => typeof h.command === "string" && isPhrenCommand(h.command))
+      );
+      if (data.hooks[event].length === 0) delete data.hooks[event];
+    }
+    if (Object.keys(data.hooks).length === 0) delete data.hooks;
+  }
+});
+
+// ── Claude Code ~/.claude.json: remove MCP server ──
+const claudeJson = homePath(".claude.json");
+patchJson(claudeJson, (data) => {
+  if (data.mcpServers?.phren) delete data.mcpServers.phren;
+});
+
+// ── VS Code MCP configs ──
+const vscodeMcpCandidates = [
+  homePath(".vscode-server", "data", "User", "mcp.json"),
+  homePath("AppData", "Roaming", "Code", "User", "mcp.json"),
+  homePath(".config", "Code", "User", "mcp.json"),
+];
+for (const mcpFile of vscodeMcpCandidates) {
+  patchJson(mcpFile, (data) => {
+    // servers array format
+    if (Array.isArray(data.servers)) {
+      data.servers = data.servers.filter((s) => s.name !== "phren");
+    }
+    // mcpServers object format
+    if (data.mcpServers?.phren) delete data.mcpServers.phren;
+  });
+}
+
+// ── Cursor MCP config ──
+const cursorMcpCandidates = [
+  homePath(".cursor", "mcp.json"),
+];
+for (const mcpFile of cursorMcpCandidates) {
+  patchJson(mcpFile, (data) => {
+    if (data.mcpServers?.phren) delete data.mcpServers.phren;
+  });
+}
+
+// ── Cursor hooks ──
+const cursorHooks = homePath(".cursor", "hooks.json");
+patchJson(cursorHooks, (data) => {
+  for (const key of ["sessionStart", "beforeSubmitPrompt", "stop"]) {
+    if (data[key]?.command && typeof data[key].command === "string" && isPhrenCommand(data[key].command)) {
+      delete data[key];
+    }
+  }
+});
+
+// ── Copilot hooks ──
+const copilotHooks = homePath(".github", "hooks", "phren.json");
+if (fs.existsSync(copilotHooks)) {
+  try { fs.unlinkSync(copilotHooks); } catch { /* best-effort */ }
+}
+
+console.log("phren: cleaned up hooks and MCP config from agent settings.");

package/starter/global/skills/pipeline.md

@@ -1,35 +0,0 @@
----
-name: pipeline
-description: Tell Claude which stage of development you're in and get guidance on what to focus on next.
----
-# /pipeline - Where am I in the workflow
-
-Tell Claude which stage of development you're in, and get guidance on what to focus on next.
-
-## Stages
-
-1. **planning** - sketching ideas, designing, deciding what to build
-2. **coding** - writing implementation, building features
-3. **testing** - running tests, verifying behavior, catching bugs
-4. **review** - code review, feedback, making sure it's ready
-5. **shipped** - released, deployed, users have it
-
-## What to do
-
-1. Look at recent git commits to understand what's been done recently.
-2. Check open files in the editor to see what's actively being worked on.
-3. Ask the user: "What stage are you in?" if unclear.
-4. Tell the user:
-   - **Current stage**: e.g. "You're in the coding stage"
-   - **What to focus on next**: e.g. "Once you finish this component, write tests for it. Don't move to review until tests pass."
-
-## Examples
-
-- "You've got 10 failing tests. You're in testing. Run tests again after each fix, don't batch them."
-- "You've got code ready but no CHANGELOG entry. That's review stage. Update the changelog, then you're ready to ship."
-- "You've got 3 open PRs awaiting feedback. You're in review. Respond to comments or start something new while you wait."
-
-## Customize
-
-- Adjust the stages to match your workflow (you might have a "documentation" or "deployment" stage)
-- Add what "done" means for each stage in your project

package/starter/global/skills/release.md

@@ -1,35 +0,0 @@
----
-name: release
-description: Get from "code is ready" to "users have it" with a version bump, changelog, tag, and publish checklist.
----
-# /release - Ship a version
-
-Get from "code is ready" to "users have it" with a checklist.
-
-## Steps
-
-1. **Confirm version bump**: Ask for patch, minor, or major (if not specified). Auto-detect from git history or ask the user.
-2. **Update CHANGELOG.md**: List what changed in this release. Format varies (keep-changelog, conventional commits, etc).
-3. **Bump version**: Update package.json, Cargo.toml, pyproject.toml, or whatever your project uses.
-4. **Git tag**: Create a git tag: `git tag vX.Y.Z` and push it.
-5. **Publish**: Run your publish command (`npm publish`, `cargo publish`, `poetry publish`, etc).
-
-## Example flow
-
-```
-You: "/release"
-Claude: "What version bump? (patch/minor/major)"
-You: "minor"
-Claude: "Got it. You're going from 1.2.3 to 1.3.0.
-  - Updated CHANGELOG.md with new features
-  - Bumped version in package.json
-  - Created tag v1.3.0
-  - Published to npm
-  Ready to verify it's live?"
-```
-
-## Customize
-
-- Update the publish command for your stack (e.g. `cargo publish` for Rust, `twine upload` for Python)
-- Adjust changelog format to match your conventions
-- Add any pre-publish checks you need (tests, linting, etc)