Replace Pi tool registrations with skills and CLI integration

- Remove all manually registered Pi tools (alpha_search, alpha_get_paper,
  alpha_ask_paper, alpha_annotate_paper, alpha_list_annotations,
  alpha_read_code, session_search, preview_file) and their wrappers
  (alpha.ts, preview.ts, session-search.ts, alpha-tools.test.ts)
- Add Pi skill files for alpha-research, session-search, preview,
  modal-compute, and runpod-compute in skills/
- Sync skills to ~/.feynman/agent/skills/ on startup via syncBundledAssets
- Add node_modules/.bin to Pi subprocess PATH so alpha CLI is accessible
- Add /outputs extension command to browse research artifacts via dialog
- Add Modal and RunPod as execution environments in /replicate and
  /autoresearch prompts
- Remove redundant /alpha-login /alpha-logout /alpha-status REPL commands
  (feynman alpha CLI still works)
- Update README, researcher agent, metadata, and website docs

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

prompts/autoresearch.md

@@ -27,6 +27,8 @@ Ask the user where to run:
 - **New git branch** — create a branch so main stays clean
 - **Virtual environment** — create an isolated venv/conda env first
 - **Docker** — run experiment code inside an isolated Docker container
+- **Modal** — run on Modal's serverless GPU infrastructure. Write Modal-decorated scripts and execute with `modal run`. Best for GPU-heavy benchmarks with no persistent state between iterations. Requires `modal` CLI.
+- **RunPod** — provision a GPU pod via `runpodctl` and run iterations there over SSH. Best for experiments needing persistent state, large datasets, or SSH access between iterations. Requires `runpodctl` CLI.
 
 Do not proceed without a clear answer.