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>

metadata/commands.mjs

@@ -37,9 +37,7 @@ export function readPromptSpecs(appRoot) {
 export const extensionCommandSpecs = [
 	{ name: "help", args: "", section: "Project & Session", description: "Show grouped Feynman commands and prefill the editor with a selected command.", publicDocs: true },
 	{ name: "init", args: "", section: "Project & Session", description: "Bootstrap AGENTS.md and session-log folders for a research project.", publicDocs: true },
-	{ name: "alpha-login", args: "", section: "Setup", description: "Sign in to alphaXiv from inside Feynman.", publicDocs: true },
-	{ name: "alpha-status", args: "", section: "Setup", description: "Show alphaXiv authentication status.", publicDocs: true },
-	{ name: "alpha-logout", args: "", section: "Setup", description: "Clear alphaXiv auth from inside Feynman.", publicDocs: true },
+	{ name: "outputs", args: "", section: "Project & Session", description: "Browse all research artifacts (papers, outputs, experiments, notes).", publicDocs: true },
 ];
 
 export const livePackageCommandGroups = [