Overhaul Feynman harness: streamline agents, prompts, and extensions

Remove legacy chains, skills, and config modules. Add citation agent,
SYSTEM.md, modular research-tools extension, and web-access layer.
Add ralph-wiggum to Pi package stack for long-running loops.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

extensions/research-tools/alpha.ts

@@ -0,0 +1,211 @@
+import {
+	annotatePaper,
+	askPaper,
+	clearPaperAnnotation,
+	disconnect,
+	getPaper,
+	getUserName as getAlphaUserName,
+	isLoggedIn as isAlphaLoggedIn,
+	listPaperAnnotations,
+	login as loginAlpha,
+	logout as logoutAlpha,
+	readPaperCode,
+	searchPapers,
+} from "@companion-ai/alpha-hub/lib";
+import type { ExtensionAPI } from "@mariozechner/pi-coding-agent";
+import { Type } from "@sinclair/typebox";
+
+import { formatToolText } from "./shared.js";
+
+export function registerAlphaCommands(pi: ExtensionAPI): void {
+	pi.registerCommand("alpha-login", {
+		description: "Sign in to alphaXiv from inside Feynman.",
+		handler: async (_args, ctx) => {
+			if (isAlphaLoggedIn()) {
+				const name = getAlphaUserName();
+				ctx.ui.notify(name ? `alphaXiv already connected as ${name}` : "alphaXiv already connected", "info");
+				return;
+			}
+
+			await loginAlpha();
+			const name = getAlphaUserName();
+			ctx.ui.notify(name ? `alphaXiv connected as ${name}` : "alphaXiv login complete", "info");
+		},
+	});
+
+	pi.registerCommand("alpha-logout", {
+		description: "Clear alphaXiv auth from inside Feynman.",
+		handler: async (_args, ctx) => {
+			logoutAlpha();
+			ctx.ui.notify("alphaXiv auth cleared", "info");
+		},
+	});
+
+	pi.registerCommand("alpha-status", {
+		description: "Show alphaXiv authentication status.",
+		handler: async (_args, ctx) => {
+			if (!isAlphaLoggedIn()) {
+				ctx.ui.notify("alphaXiv not connected", "warning");
+				return;
+			}
+
+			const name = getAlphaUserName();
+			ctx.ui.notify(name ? `alphaXiv connected as ${name}` : "alphaXiv connected", "info");
+		},
+	});
+}
+
+export function registerAlphaTools(pi: ExtensionAPI): void {
+	pi.registerTool({
+		name: "alpha_search",
+		label: "Alpha Search",
+		description: "Search papers through alphaXiv using semantic, keyword, both, agentic, or all retrieval modes.",
+		parameters: Type.Object({
+			query: Type.String({ description: "Paper search query." }),
+			mode: Type.Optional(
+				Type.String({
+					description: "Search mode: semantic, keyword, both, agentic, or all.",
+				}),
+			),
+		}),
+		async execute(_toolCallId, params) {
+			try {
+				const result = await searchPapers(params.query, params.mode?.trim() || "all");
+				return {
+					content: [{ type: "text", text: formatToolText(result) }],
+					details: result,
+				};
+			} finally {
+				await disconnect();
+			}
+		},
+	});
+
+	pi.registerTool({
+		name: "alpha_get_paper",
+		label: "Alpha Get Paper",
+		description: "Fetch a paper report or full text, plus any local annotation, using alphaXiv.",
+		parameters: Type.Object({
+			paper: Type.String({
+				description: "arXiv ID, arXiv URL, or alphaXiv URL.",
+			}),
+			fullText: Type.Optional(
+				Type.Boolean({
+					description: "Return raw full text instead of the AI report.",
+				}),
+			),
+		}),
+		async execute(_toolCallId, params) {
+			try {
+				const result = await getPaper(params.paper, { fullText: params.fullText });
+				return {
+					content: [{ type: "text", text: formatToolText(result) }],
+					details: result,
+				};
+			} finally {
+				await disconnect();
+			}
+		},
+	});
+
+	pi.registerTool({
+		name: "alpha_ask_paper",
+		label: "Alpha Ask Paper",
+		description: "Ask a targeted question about a paper using alphaXiv's PDF analysis.",
+		parameters: Type.Object({
+			paper: Type.String({
+				description: "arXiv ID, arXiv URL, or alphaXiv URL.",
+			}),
+			question: Type.String({
+				description: "Question to ask about the paper.",
+			}),
+		}),
+		async execute(_toolCallId, params) {
+			try {
+				const result = await askPaper(params.paper, params.question);
+				return {
+					content: [{ type: "text", text: formatToolText(result) }],
+					details: result,
+				};
+			} finally {
+				await disconnect();
+			}
+		},
+	});
+
+	pi.registerTool({
+		name: "alpha_annotate_paper",
+		label: "Alpha Annotate Paper",
+		description: "Write or clear a persistent local annotation for a paper.",
+		parameters: Type.Object({
+			paper: Type.String({
+				description: "Paper ID to annotate.",
+			}),
+			note: Type.Optional(
+				Type.String({
+					description: "Annotation text. Omit when clear=true.",
+				}),
+			),
+			clear: Type.Optional(
+				Type.Boolean({
+					description: "Clear the existing annotation instead of writing one.",
+				}),
+			),
+		}),
+		async execute(_toolCallId, params) {
+			const result = params.clear
+				? await clearPaperAnnotation(params.paper)
+				: params.note
+					? await annotatePaper(params.paper, params.note)
+					: (() => {
+							throw new Error("Provide either note or clear=true.");
+						})();
+
+			return {
+				content: [{ type: "text", text: formatToolText(result) }],
+				details: result,
+			};
+		},
+	});
+
+	pi.registerTool({
+		name: "alpha_list_annotations",
+		label: "Alpha List Annotations",
+		description: "List all persistent local paper annotations.",
+		parameters: Type.Object({}),
+		async execute() {
+			const result = await listPaperAnnotations();
+			return {
+				content: [{ type: "text", text: formatToolText(result) }],
+				details: result,
+			};
+		},
+	});
+
+	pi.registerTool({
+		name: "alpha_read_code",
+		label: "Alpha Read Code",
+		description: "Read files from a paper's GitHub repository through alphaXiv.",
+		parameters: Type.Object({
+			githubUrl: Type.String({
+				description: "GitHub repository URL for the paper implementation.",
+			}),
+			path: Type.Optional(
+				Type.String({
+					description: "Repository path to inspect. Use / for the repo overview.",
+				}),
+			),
+		}),
+		async execute(_toolCallId, params) {
+			try {
+				const result = await readPaperCode(params.githubUrl, params.path?.trim() || "/");
+				return {
+					content: [{ type: "text", text: formatToolText(result) }],
+					details: result,
+				};
+			} finally {
+				await disconnect();
+			}
+		},
+	});
+}