Migrate monorepo from npm to pnpm

[amrmelsayed]

Summary

• Strict dependency isolation prevents phantom dependency issues as the monorepo grows (vscode extension, future desktop app)
• Faster CI installs via content-addressable store and pnpm caching
• Smaller node_modules through symlinked global store instead of copies
• workspace:* protocol auto-replaces with real versions at publish time
• Built-in workspace filtering (--filter) for targeted package operations

Changes

• Add pnpm-workspace.yaml with onlyBuiltDependencies for native modules (node-pty, better-sqlite3, esbuild, protobufjs)
• Convert workspace deps from "*" to "workspace:*" protocol
• Update all package.json scripts from npm run to pnpm
• Replace npm-run-all with pnpm's built-in parallel regex matching in vscode package
• Update CI workflows (test, e2e, dashboard-e2e) with pnpm/action-setup and cache: 'pnpm'
• Update release protocol, CLAUDE.md, AGENTS.md for pnpm commands
• Delete package-lock.json, add pnpm-lock.yaml
• post-release-e2e.yml intentionally unchanged (tests published npm packages)

After merge — developer setup

npm install -g pnpm@latest   # if not already installed
rm -rf node_modules
pnpm install

Test plan

• pnpm install succeeds from repo root
• pnpm build succeeds in packages/codev (includes dashboard build + skeleton copy)
• All 2442 unit tests pass
• node-pty postinstall hook resolves correctly under pnpm
• Native modules (better-sqlite3, node-pty, esbuild) build successfully
• CI workflows pass on this PR
• Tower starts and dashboard loads after global install