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>

website/src/content/docs/reference/cli-commands.md

@@ -37,7 +37,7 @@ These commands manage your model provider configuration. The `model set` command
 | `feynman alpha logout` | Clear alphaXiv auth |
 | `feynman alpha status` | Check alphaXiv auth status |
 
-AlphaXiv authentication enables Feynman to search and retrieve papers, access discussion threads, and pull citation metadata. You can also manage AlphaXiv auth from inside the REPL with `/alpha-login`, `/alpha-status`, and `/alpha-logout`.
+AlphaXiv authentication enables Feynman to search and retrieve papers, access discussion threads, and pull citation metadata. The `alpha` CLI is also available directly in the agent shell for paper search, Q&A, and code inspection.
 
 ## Package management