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>

extensions/research-tools.ts

@@ -1,9 +1,8 @@
 import type { ExtensionAPI } from "@mariozechner/pi-coding-agent";
 
-import { registerAlphaCommands, registerAlphaTools } from "./research-tools/alpha.js";
 import { installFeynmanHeader } from "./research-tools/header.js";
 import { registerHelpCommand } from "./research-tools/help.js";
-import { registerInitCommand, registerPreviewTool, registerSessionSearchTool } from "./research-tools/project.js";
+import { registerInitCommand, registerOutputsCommand } from "./research-tools/project.js";
 
 export default function researchTools(pi: ExtensionAPI): void {
 	const cache: { agentSummaryPromise?: Promise<{ agents: string[]; chains: string[] }> } = {};
@@ -16,10 +15,7 @@ export default function researchTools(pi: ExtensionAPI): void {
 		await installFeynmanHeader(pi, ctx, cache);
 	});
 
-	registerAlphaCommands(pi);
 	registerHelpCommand(pi);
 	registerInitCommand(pi);
-	registerSessionSearchTool(pi);
-	registerAlphaTools(pi);
-	registerPreviewTool(pi);
+	registerOutputsCommand(pi);
 }