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/shared.ts

@@ -1,5 +1,4 @@
 import { readFileSync } from "node:fs";
-import { homedir } from "node:os";
 import { dirname, resolve as resolvePath } from "node:path";
 import { fileURLToPath } from "node:url";
 
@@ -15,30 +14,3 @@ export const FEYNMAN_VERSION = (() => {
 })();
 
 export { FEYNMAN_ASCII_LOGO as FEYNMAN_AGENT_LOGO } from "../../logo.mjs";
-
-export const FEYNMAN_RESEARCH_TOOLS = [
-	"alpha_search",
-	"alpha_get_paper",
-	"alpha_ask_paper",
-	"alpha_annotate_paper",
-	"alpha_list_annotations",
-	"alpha_read_code",
-	"session_search",
-	"preview_file",
-];
-
-export function collapseExcessBlankLines(text: string): string {
-	return text.replace(/\r\n/g, "\n").replace(/\n{3,}/g, "\n\n").trim();
-}
-
-export function formatToolText(result: unknown): string {
-	const text = typeof result === "string" ? result : JSON.stringify(result, null, 2);
-	return collapseExcessBlankLines(text);
-}
-
-export function getFeynmanHome(): string {
-	const agentDir = process.env.FEYNMAN_CODING_AGENT_DIR ??
-		process.env.PI_CODING_AGENT_DIR ??
-		resolvePath(homedir(), ".feynman", "agent");
-	return dirname(agentDir);
-}