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>

tests/alpha-tools.test.ts

@@ -1,86 +0,0 @@
-import test from "node:test";
-import assert from "node:assert/strict";
-
-import { formatAlphaSearchContext, sanitizeAlphaSearchPayload } from "../extensions/research-tools/alpha.js";
-import { formatToolText } from "../extensions/research-tools/shared.js";
-
-test("sanitizeAlphaSearchPayload drops raw alpha search text while keeping parsed hits", () => {
-	const payload = sanitizeAlphaSearchPayload({
-		query: "scaling laws",
-		mode: "all",
-		semantic: {
-			raw: "\n\n\n1. **Paper A**\n- Abstract: noisy raw block",
-			results: [
-				{
-					rank: 1,
-					title: "Paper A",
-					publishedAt: "2025-09-28",
-					organizations: "Stanford University, EPFL",
-					authors: "A. Author, B. Author",
-					abstract: "Line one.\n\n\nLine two.",
-					arxivId: "2509.24012",
-					arxivUrl: "https://arxiv.org/abs/2509.24012",
-					alphaXivUrl: "https://www.alphaxiv.org/overview/2509.24012",
-					raw: "internal raw block that should be dropped",
-				},
-			],
-		},
-		keyword: {
-			raw: "\n\n\nNoisy keyword fallback",
-			results: [],
-		},
-	});
-
-	assert.deepEqual(payload, {
-		query: "scaling laws",
-		mode: "all",
-		semantic: {
-			count: 1,
-			results: [
-				{
-					rank: 1,
-					title: "Paper A",
-					publishedAt: "2025-09-28",
-					organizations: "Stanford University, EPFL",
-					authors: "A. Author, B. Author",
-					abstract: "Line one. Line two.",
-					arxivId: "2509.24012",
-					arxivUrl: "https://arxiv.org/abs/2509.24012",
-					alphaXivUrl: "https://www.alphaxiv.org/overview/2509.24012",
-				},
-			],
-		},
-		keyword: {
-			count: 0,
-			results: [],
-			note: "Noisy keyword fallback",
-		},
-	});
-});
-
-test("formatAlphaSearchContext emits compact model-facing text without raw JSON escapes", () => {
-	const text = formatAlphaSearchContext({
-		query: "scaling laws",
-		mode: "semantic",
-		results: [
-			{
-				rank: 1,
-				title: "Paper A",
-				abstract: "First line.\n\n\nSecond line.",
-				arxivId: "2509.24012",
-				raw: "should not appear",
-			},
-		],
-		raw: "\n\n\nvery noisy raw payload",
-	});
-
-	assert.match(text, /query: scaling laws/);
-	assert.match(text, /1\. Paper A/);
-	assert.match(text, /abstract: First line\. Second line\./);
-	assert.ok(!text.includes("\\n"));
-	assert.ok(!text.includes("raw"));
-});
-
-test("formatToolText collapses excess blank lines in plain strings", () => {
-	assert.equal(formatToolText("alpha\n\n\n\nbeta"), "alpha\n\nbeta");
-});