Migrate monorepo from npm to pnpm

.github/workflows/dashboard-e2e.yml

@@ -13,26 +13,29 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
+      - name: Install pnpm
+        uses: pnpm/action-setup@v4
+
       - name: Setup Node.js
         uses: actions/setup-node@v4
         with:
           node-version: '20'
+          cache: 'pnpm'
 
       - name: Install dependencies
-        working-directory: packages/codev
-        run: npm install
+        run: pnpm install
 
       - name: Build package
         working-directory: packages/codev
-        run: npm run build
+        run: pnpm build
 
       - name: Install Playwright browsers
         working-directory: packages/codev
-        run: npx playwright install chromium
+        run: pnpm exec playwright install chromium
 
       - name: Run Playwright tests
         working-directory: packages/codev
         env:
           TOWER_ARCHITECT_CMD: bash
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: npx playwright test --retries 3
+        run: pnpm exec playwright test --retries 3

.github/workflows/e2e.yml

@@ -22,19 +22,22 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
+      - name: Install pnpm
+        uses: pnpm/action-setup@v4
+
       - name: Setup Node.js
         uses: actions/setup-node@v4
         with:
           node-version: '20'
+          cache: 'pnpm'
 
-      - name: Install package dependencies
-        working-directory: packages/codev
-        run: npm install
+      - name: Install dependencies
+        run: pnpm install
 
       - name: Build package
         working-directory: packages/codev
-        run: npm run build
+        run: pnpm build
 
       - name: Run CLI integration tests
         working-directory: packages/codev
-        run: npx vitest run --config vitest.cli.config.ts
+        run: pnpm exec vitest run --config vitest.cli.config.ts

.github/workflows/test.yml

@@ -13,18 +13,21 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
+      - name: Install pnpm
+        uses: pnpm/action-setup@v4
+
       - name: Setup Node.js
         uses: actions/setup-node@v4
         with:
           node-version: '20'
+          cache: 'pnpm'
 
       - name: Install dependencies
-        working-directory: packages/codev
-        run: npm install
+        run: pnpm install
 
       - name: Copy skeleton for unit tests
         working-directory: packages/codev
-        run: npm run copy-skeleton
+        run: pnpm copy-skeleton
 
       - name: Run unit tests with coverage
         working-directory: packages/codev
@@ -37,7 +40,7 @@ jobs:
           # Vitest forks pool has a known issue where the worker process crashes
           # during cleanup after all tests pass (native module teardown).
           # Capture the output and check if all test files passed.
-          npx vitest run --coverage 2>&1 | tee /tmp/vitest-output.txt; VITEST_EXIT=$?
+          pnpm exec vitest run --coverage 2>&1 | tee /tmp/vitest-output.txt; VITEST_EXIT=$?
           if [ $VITEST_EXIT -ne 0 ]; then
             # Check if all test files actually passed despite the exit code
             if grep -q "Test Files.*passed" /tmp/vitest-output.txt && ! grep -q "failed" /tmp/vitest-output.txt; then
@@ -54,22 +57,25 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
+      - name: Install pnpm
+        uses: pnpm/action-setup@v4
+
       - name: Setup Node.js
         uses: actions/setup-node@v4
         with:
           node-version: '20'
+          cache: 'pnpm'
 
       - name: Install dependencies
-        working-directory: packages/codev
-        run: npm install
+        run: pnpm install
 
       - name: Build package
         working-directory: packages/codev
-        run: npm run build
+        run: pnpm build
 
       - name: Run tower integration tests
         working-directory: packages/codev
-        run: npx vitest run --config vitest.e2e.config.ts --exclude 'src/commands/porch/__tests__/e2e/**'
+        run: pnpm exec vitest run --config vitest.e2e.config.ts --exclude 'src/commands/porch/__tests__/e2e/**'
 
   cli:
     name: CLI Integration Tests
@@ -78,22 +84,25 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
+      - name: Install pnpm
+        uses: pnpm/action-setup@v4
+
       - name: Setup Node.js
         uses: actions/setup-node@v4
         with:
           node-version: '20'
+          cache: 'pnpm'
 
       - name: Install dependencies
-        working-directory: packages/codev
-        run: npm install
+        run: pnpm install
 
       - name: Build package
         working-directory: packages/codev
-        run: npm run build
+        run: pnpm build
 
       - name: Run CLI integration tests
         working-directory: packages/codev
-        run: npx vitest run --config vitest.cli.config.ts
+        run: pnpm exec vitest run --config vitest.cli.config.ts
 
   package:
     name: Package Install Verification
@@ -102,22 +111,25 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
+      - name: Install pnpm
+        uses: pnpm/action-setup@v4
+
       - name: Setup Node.js
         uses: actions/setup-node@v4
         with:
           node-version: '20'
+          cache: 'pnpm'
 
       - name: Install dependencies
-        working-directory: packages/codev
-        run: npm install
+        run: pnpm install
 
       - name: Build package
         working-directory: packages/codev
-        run: npm run build
+        run: pnpm build
 
       - name: Pack tarball
         working-directory: packages/codev
-        run: npm pack
+        run: pnpm pack
 
       - name: Verify install from tarball
         working-directory: packages/codev

.gitignore

@@ -14,6 +14,9 @@ worktrees/
 # npm package tarballs
 *.tgz
 
+# Prevent accidental npm usage from recreating lockfile
+package-lock.json
+
 # Cleanup/maintain protocol artifacts
 # .trash/ contains soft-deleted files (bulk data, not versioned)
 codev/cleanup/.trash/

AGENTS.md

@@ -40,8 +40,8 @@ To test changes locally before publishing to npm:
 cd packages/codev
 
 # 1. Build and create tarball (Tower stays up during this)
-npm run build
-npm pack
+pnpm build
+pnpm pack
 
 # 2. Install (Tower stays up — running process already loaded old code)
 npm install -g ./cluesmith-codev-*.tgz
@@ -54,7 +54,7 @@ afx tower stop && afx tower start
 - Do NOT stop Tower before installing — unnecessary downtime
 - Do NOT delete the tarball — keep it for debugging if restart fails
 - Do NOT build between stop and start
-- Do NOT use `npm link` — it breaks global installs
+- Do NOT use `npm link` or `pnpm link` — it breaks global installs
 
 ### Testing
 
@@ -121,7 +121,7 @@ validated: [gemini, codex, claude]
 | Running tests | 10-300s | `run_in_background: true` |
 | Consultations (consult) | 60-250s | `run_in_background: true` |
 | E2E test suites | 60-600s | `run_in_background: true` |
-| npm install/build | 5-60s | `run_in_background: true` |
+| pnpm install/build | 5-60s | `run_in_background: true` |
 | Quick file reads/edits | <5s | Run normally |
 
 **Critical**: Using `&` at the end of the command does NOT work - you MUST set the `run_in_background` parameter.
@@ -217,7 +217,8 @@ project-root/
 ```
 
 ## Directory Map
-- npm install / npm run build / npm test → always run from `packages/codev/`
+- pnpm install → always run from the repository root (installs all workspace packages)
+- pnpm build / pnpm test → run from `packages/codev/` or use `pnpm --filter @cluesmith/codev build`
 - E2E tests → `packages/codev/tests/e2e/`
 - Unit tests → `packages/codev/tests/unit/`
 - Never run npm commands from the repository root unless explicitly told to.

CLAUDE.md

@@ -40,8 +40,8 @@ To test changes locally before publishing to npm:
 cd packages/codev
 
 # 1. Build and create tarball (Tower stays up during this)
-npm run build
-npm pack
+pnpm build
+pnpm pack
 
 # 2. Install (Tower stays up — running process already loaded old code)
 npm install -g ./cluesmith-codev-*.tgz
@@ -54,7 +54,7 @@ afx tower stop && afx tower start
 - Do NOT stop Tower before installing — unnecessary downtime
 - Do NOT delete the tarball — keep it for debugging if restart fails
 - Do NOT build between stop and start
-- Do NOT use `npm link` — it breaks global installs
+- Do NOT use `npm link` or `pnpm link` — it breaks global installs
 
 ### Testing
 
@@ -121,7 +121,7 @@ validated: [gemini, codex, claude]
 | Running tests | 10-300s | `run_in_background: true` |
 | Consultations (consult) | 60-250s | `run_in_background: true` |
 | E2E test suites | 60-600s | `run_in_background: true` |
-| npm install/build | 5-60s | `run_in_background: true` |
+| pnpm install/build | 5-60s | `run_in_background: true` |
 | Quick file reads/edits | <5s | Run normally |
 
 **Critical**: Using `&` at the end of the command does NOT work - you MUST set the `run_in_background` parameter.
@@ -217,7 +217,8 @@ project-root/
 ```
 
 ## Directory Map
-- npm install / npm run build / npm test → always run from `packages/codev/`
+- pnpm install → always run from the repository root (installs all workspace packages)
+- pnpm build / pnpm test → run from `packages/codev/` or use `pnpm --filter @cluesmith/codev build`
 - E2E tests → `packages/codev/tests/e2e/`
 - Unit tests → `packages/codev/tests/unit/`
 - Never run npm commands from the repository root unless explicitly told to.

codev/protocols/release/protocol.md

@@ -57,13 +57,13 @@ bats tests/e2e/
 cd packages/codev
 
 # Bump version (choose one)
-npm version patch --no-git-tag-version  # Bug fixes only
-npm version minor --no-git-tag-version  # New features
-npm version major --no-git-tag-version  # Breaking changes
+pnpm version patch --no-git-tag-version  # Bug fixes only
+pnpm version minor --no-git-tag-version  # New features
+pnpm version major --no-git-tag-version  # Breaking changes
 
 # Commit and tag
 cd ../..
-git add packages/codev/package.json packages/codev/package-lock.json
+git add packages/codev/package.json pnpm-lock.yaml
 git commit -m "Release @cluesmith/codev@X.Y.Z (Codename)"
 git tag -a vX.Y.Z -m "vX.Y.Z Codename - Brief description"
 git push && git push origin vX.Y.Z
@@ -114,7 +114,7 @@ gh release create vX.Y.Z --title "vX.Y.Z Codename" --notes-file docs/releases/vX
 ### 7. Publish to npm
 
 ```bash
-cd packages/codev && npm publish
+cd packages/codev && pnpm publish
 ```
 
 ### 8. Post to Discussion Forum
@@ -189,17 +189,17 @@ Starting with v1.7.0, minor releases use a release candidate workflow for testin
 ```bash
 # Set version to RC
 cd packages/codev
-npm version 1.7.0-rc.1 --no-git-tag-version
+pnpm version 1.7.0-rc.1 --no-git-tag-version
 
 # Commit and tag
 cd ../..
-git add packages/codev/package.json packages/codev/package-lock.json
+git add packages/codev/package.json pnpm-lock.yaml
 git commit -m "v1.7.0-rc.1"
 git tag -a v1.7.0-rc.1 -m "v1.7.0-rc.1 - Release candidate"
 git push && git push origin v1.7.0-rc.1
 
 # Publish to "next" channel (NOT "latest")
-cd packages/codev && npm publish --tag next
+cd packages/codev && pnpm publish --tag next
 ```
 
 ### RC → Stable Promotion
@@ -209,7 +209,7 @@ When an RC is validated and ready for stable release:
 ```bash
 # Bump to stable version
 cd packages/codev
-npm version 1.7.0 --no-git-tag-version
+pnpm version 1.7.0 --no-git-tag-version
 
 # Follow standard release process (steps 4-9 above)
 ```
@@ -243,15 +243,15 @@ git cherry-pick <commit-hash>
 
 # Bump patch version
 cd packages/codev
-npm version patch --no-git-tag-version
+pnpm version patch --no-git-tag-version
 
 # Commit, tag, and publish
 cd ../..
-git add packages/codev/package.json packages/codev/package-lock.json
+git add packages/codev/package.json pnpm-lock.yaml
 git commit -m "v1.6.1 - Backport: <fix description>"
 git tag -a v1.6.1 -m "v1.6.1 - Backport fix"
 git push origin release/1.6.x && git push origin v1.6.1
-cd packages/codev && npm publish
+cd packages/codev && pnpm publish
 ```
 
 ### When to Use RCs

hooks/pre-commit

@@ -26,11 +26,11 @@ if [[ -d "agent-farm" && -f "agent-farm/package.json" ]]; then
     # Check if node_modules exists, install if needed
     if [[ ! -d "agent-farm/node_modules" ]]; then
         echo "Installing agent-farm dependencies..."
-        (cd agent-farm && npm install --silent)
+        (cd agent-farm && pnpm install --silent)
     fi
 
     # Run TypeScript build and tests
-    if ! (cd agent-farm && npm run build --silent && npm test -- --run); then
+    if ! (cd agent-farm && pnpm build --silent && pnpm test -- --run); then
         echo "❌ agent-farm tests failed - commit aborted"
         echo ""
         echo "To skip this check (not recommended):"