chore: release prep v0.12.0 — version bumps, package metadata, CI fix

Phase 1 - Repo Hygiene:
- Fix CI workflow stale path: services/mcp-server → packages/mcp-server
- Create ep-cli README.md with installation and command docs

Phase 2 - Package Prep:
- Add files, publishConfig, repository, bugs, homepage, engines to ep-cli
- Add publishConfig, repository, bugs, homepage to pipeline-state
- Update @effect/schema dep 0.68 → 0.75 in pipeline-state
- Exclude dist/__tests__ from toolkit package
- Add repository, bugs, homepage, engines to ep-shared-services
- Copy LICENSE to all publishable packages

Phase 3 - Versions & Changelogs:
- Root: 0.11.0 → 0.12.0
- toolkit: 0.3.0 → 0.4.0
- ep-cli: 0.2.0 → 0.3.0
- ep-shared-services: 1.0.0 → 1.0.1
- pipeline-state: 1.1.0 → 1.1.1
- mcp-server: 0.7.6 → 0.7.7
- Update/create changelogs for all packages
- Delete stale changeset files

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>