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/slash-commands.md

@@ -31,21 +31,12 @@ These are the primary commands you will use day-to-day. Each workflow dispatches
 | `/jobs` | Inspect active background work: running processes, scheduled follow-ups, and active watches |
 | `/help` | Show grouped Feynman commands and prefill the editor with a selected command |
 | `/init` | Bootstrap `AGENTS.md` and session-log folders for a new research project |
+| `/outputs` | Browse all research artifacts (papers, outputs, experiments, notes) |
 | `/search` | Search prior session transcripts for past research and findings |
 | `/preview` | Preview the current artifact as rendered HTML or PDF |
 
 Session management commands help you organize ongoing work. The `/log` command is particularly useful at the end of a research session to capture what was accomplished and what remains.
 
-## Setup commands
-
-| Command | Description |
-| --- | --- |
-| `/alpha-login` | Sign in to alphaXiv from inside the REPL |
-| `/alpha-status` | Show alphaXiv authentication status |
-| `/alpha-logout` | Clear alphaXiv auth from inside the REPL |
-
-These provide a convenient way to manage alphaXiv authentication without leaving the REPL.
-
 ## Running workflows from the CLI
 
 All research workflow slash commands can also be run directly from the command line: