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>

skills/alpha-research/SKILL.md

@@ -0,0 +1,42 @@
+---
+name: alpha-research
+description: Search, read, and query research papers via the `alpha` CLI (alphaXiv-backed). Use when the user asks about academic papers, wants to find research on a topic, needs to read a specific paper, ask questions about a paper, inspect a paper's code repository, or manage paper annotations.
+---
+
+# Alpha Research CLI
+
+Use the `alpha` CLI via bash for all paper research operations.
+
+## Commands
+
+| Command | Description |
+|---------|-------------|
+| `alpha search "<query>"` | Search papers. Modes: `--mode semantic`, `--mode keyword`, `--mode agentic` |
+| `alpha get <arxiv-id-or-url>` | Fetch paper content and any local annotation |
+| `alpha get --full-text <arxiv-id>` | Get raw full text instead of AI report |
+| `alpha ask <arxiv-id> "<question>"` | Ask a question about a paper's PDF |
+| `alpha code <github-url> [path]` | Read files from a paper's GitHub repo. Use `/` for overview |
+| `alpha annotate <paper-id> "<note>"` | Save a persistent annotation on a paper |
+| `alpha annotate --clear <paper-id>` | Remove an annotation |
+| `alpha annotate --list` | List all annotations |
+
+## Auth
+
+Run `alpha login` to authenticate with alphaXiv. Check status with `alpha status`.
+
+## Examples
+
+```bash
+alpha search "transformer scaling laws"
+alpha search --mode agentic "efficient attention mechanisms for long context"
+alpha get 2106.09685
+alpha ask 2106.09685 "What optimizer did they use?"
+alpha code https://github.com/karpathy/nanoGPT src/model.py
+alpha annotate 2106.09685 "Key paper on LoRA - revisit for adapter comparison"
+```
+
+## When to use
+
+- Academic paper search, reading, Q&A → `alpha`
+- Current topics (products, releases, docs) → web search tools
+- Mixed topics → combine both