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>

src/bootstrap/sync.ts

@@ -130,6 +130,7 @@ export function syncBundledAssets(appRoot: string, agentDir: string): BootstrapS
 
 	syncManagedFiles(resolve(appRoot, ".feynman", "themes"), resolve(agentDir, "themes"), state, result);
 	syncManagedFiles(resolve(appRoot, ".feynman", "agents"), resolve(agentDir, "agents"), state, result);
+	syncManagedFiles(resolve(appRoot, "skills"), resolve(agentDir, "skills"), state, result);
 
 	writeBootstrapState(statePath, state);
 	return result;

src/pi/runtime.ts

@@ -29,6 +29,7 @@ export function resolvePiPaths(appRoot: string) {
 		promptTemplatePath: resolve(appRoot, "prompts"),
 		systemPromptPath: resolve(appRoot, ".feynman", "SYSTEM.md"),
 		piWorkspaceNodeModulesPath: resolve(appRoot, ".feynman", "npm", "node_modules"),
+		nodeModulesBinPath: resolve(appRoot, "node_modules", ".bin"),
 	};
 }
 
@@ -77,8 +78,12 @@ export function buildPiArgs(options: PiRuntimeOptions): string[] {
 export function buildPiEnv(options: PiRuntimeOptions): NodeJS.ProcessEnv {
 	const paths = resolvePiPaths(options.appRoot);
 
+	const currentPath = process.env.PATH ?? "";
+	const binPath = paths.nodeModulesBinPath;
+
 	return {
 		...process.env,
+		PATH: `${binPath}:${currentPath}`,
 		FEYNMAN_VERSION: options.feynmanVersion,
 		FEYNMAN_SESSION_DIR: options.sessionDir,
 		FEYNMAN_MEMORY_DIR: resolve(dirname(options.feynmanAgentDir), "memory"),