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
 

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:

website/src/content/docs/tools/alphaxiv.md

@@ -21,27 +21,32 @@ Check your authentication status:
 feynman alpha status
 ```
 
-You can also manage AlphaXiv auth from inside the REPL with `/alpha-login`, `/alpha-status`, and `/alpha-logout`.
-
 ## What it provides
 
 AlphaXiv gives Feynman access to several capabilities that power the research workflows:
 
-- **Paper search** -- Find papers by topic, author, keyword, or arXiv ID
-- **Full-text retrieval** -- Download and parse complete PDFs for in-depth reading
-- **Citation metadata** -- Access citation counts, references, and citation chains
-- **Discussion threads** -- Read community discussions and annotations on papers
-- **Related papers** -- Discover connected work through citation graphs and recommendations
+- **Paper search** -- Find papers by topic, author, keyword, or arXiv ID (`alpha search`)
+- **Full-text retrieval** -- Download and parse complete PDFs for in-depth reading (`alpha get`)
+- **Paper Q&A** -- Ask targeted questions about a paper's content (`alpha ask`)
+- **Code inspection** -- Read files from a paper's linked GitHub repository (`alpha code`)
+- **Annotations** -- Persistent local notes on papers across sessions (`alpha annotate`)
 
 ## How it is used
 
-You do not invoke AlphaXiv directly in most cases. The researcher agent uses it automatically during workflows like deep research, literature review, and peer review. When you provide an arXiv ID (like `arxiv:2401.12345`), Feynman fetches the paper through AlphaXiv.
+Feynman ships an `alpha-research` skill that teaches the agent to use the `alpha` CLI for paper operations. The researcher agent uses it automatically during workflows like deep research, literature review, and peer review. When you provide an arXiv ID (like `2401.12345`), the agent fetches the paper via `alpha get`.
 
-AlphaXiv search is especially powerful when combined with citation chaining. The researcher agent can follow references from a relevant paper to discover foundational work, then follow forward citations to find papers that built on it. This produces a much more complete picture than keyword search alone.
+You can also use the `alpha` CLI directly from the terminal:
+
+```bash
+alpha search "scaling laws"
+alpha get 2401.12345
+alpha ask 2401.12345 "What optimizer did they use?"
+alpha code https://github.com/org/repo src/model.py
+```
 
 ## Configuration
 
-AlphaXiv configuration is managed through the CLI commands listed above. Authentication tokens are stored in `~/.feynman/auth/` and persist across sessions. No additional configuration is needed beyond logging in.
+Authentication tokens are stored in `~/.feynman/auth/` and persist across sessions. No additional configuration is needed beyond logging in.
 
 ## Without AlphaXiv