Finalize remaining repo updates

README.md

@@ -1,44 +1,59 @@
-# Feynman
+<p align="center">
+  <a href="https://feynman.is">
+    <img src="assets/hero.png" alt="Feynman CLI" width="800" />
+  </a>
+</p>
+<p align="center">The open source AI research agent.</p>
+<p align="center">
+  <a href="https://feynman.is/docs"><img alt="Docs" src="https://img.shields.io/badge/docs-feynman.is-0d9668?style=flat-square" /></a>
+  <a href="https://www.npmjs.com/package/@companion-ai/feynman"><img alt="npm" src="https://img.shields.io/npm/v/@companion-ai/feynman?style=flat-square" /></a>
+  <a href="https://github.com/getcompanion-ai/feynman/blob/main/LICENSE"><img alt="License" src="https://img.shields.io/github/license/getcompanion-ai/feynman?style=flat-square" /></a>
+</p>
 
-The open source AI research agent
+---
+
+### Installation
 
 ```bash
 curl -fsSL https://feynman.is/install | bash
 ```
 
 ```powershell
+# Windows
 irm https://feynman.is/install.ps1 | iex
 ```
 
-Or install the npm fallback:
-
 ```bash
+# npm fallback
 npm install -g @companion-ai/feynman
 ```
 
-```bash
-feynman setup
-feynman
+Then run `feynman setup` to configure your model and get started.
+
+---
+
+### What you type → what happens
+
+```
+$ feynman "what do we know about scaling laws"
+→ Searches papers and web, produces a cited research brief
+
+$ feynman deepresearch "mechanistic interpretability"
+→ Multi-agent investigation with parallel researchers, synthesis, verification
+
+$ feynman lit "RLHF alternatives"
+→ Literature review with consensus, disagreements, open questions
+
+$ feynman audit 2401.12345
+→ Compares paper claims against the public codebase
+
+$ feynman replicate "chain-of-thought improves math"
+→ Asks where to run, then builds a replication plan
 ```
 
-Feynman works directly inside your folder or repo. For long-running work, keep the stable repo contract in `AGENTS.md`, the current task brief in `outputs/.plans/`, and the chronological lab notebook in `CHANGELOG.md`.
-
 ---
 
-## What you type → what happens
-
-| Prompt | Result |
-| --- | --- |
-| `feynman "what do we know about scaling laws"` | Searches papers and web, produces a cited research brief |
-| `feynman deepresearch "mechanistic interpretability"` | Multi-agent investigation with parallel researchers, synthesis, verification |
-| `feynman lit "RLHF alternatives"` | Literature review with consensus, disagreements, open questions |
-| `feynman audit 2401.12345` | Compares paper claims against the public codebase |
-| `feynman replicate "chain-of-thought improves math"` | Asks where to run, then builds a replication plan |
-| `feynman "summarize this PDF" --prompt paper.pdf` | One-shot mode, no REPL |
-
----
-
-## Workflows
+### Workflows
 
 Ask naturally or use slash commands as shortcuts.
 
@@ -56,9 +71,9 @@ Ask naturally or use slash commands as shortcuts.
 
 ---
 
-## Agents
+### Agents
 
-Four bundled research agents, dispatched automatically or via subagent commands.
+Four bundled research agents, dispatched automatically.
 
 - **Researcher** — gather evidence across papers, web, repos, docs
 - **Reviewer** — simulated peer review with severity-graded feedback
@@ -67,42 +82,23 @@ Four bundled research agents, dispatched automatically or via subagent commands.
 
 ---
 
-## Tools
+### Tools
 
 - **[AlphaXiv](https://www.alphaxiv.org/)** — paper search, Q&A, code reading, persistent annotations
 - **Docker** — isolated container execution for safe experiments on your machine
-- **Web search** — Gemini or Perplexity, zero-config default via signed-in Chromium
-- **Session search** — optional indexed recall across prior research sessions
+- **Web search** — Gemini or Perplexity, zero-config default
+- **Session search** — indexed recall across prior research sessions
 - **Preview** — browser and PDF export of generated artifacts
 
 ---
 
-## CLI
+### How it works
 
-```bash
-feynman                             # REPL
-feynman setup                       # guided setup
-feynman doctor                      # diagnose everything
-feynman status                      # current config summary
-feynman model login [provider]      # model auth
-feynman model set <provider/model>  # set default model
-feynman alpha login                 # alphaXiv auth
-feynman packages list               # core vs optional packages
-feynman packages install memory     # opt into heavier packages on demand
-feynman search status               # web search config
-```
+Built on [Pi](https://github.com/badlogic/pi-mono) for the agent runtime, [alphaXiv](https://www.alphaxiv.org/) for paper search and analysis, and [Docker](https://www.docker.com/) for isolated local execution. Every output is source-grounded — claims link to papers, docs, or repos with direct URLs.
 
 ---
 
-## How it works
-
-Built on [Pi](https://github.com/badlogic/pi-mono) for the agent runtime, [alphaXiv](https://www.alphaxiv.org/) for paper search and analysis, and [Docker](https://www.docker.com/) for isolated local execution
-
-Every output is source-grounded — claims link to papers, docs, or repos with direct URLs
-
----
-
-## Contributing
+### Contributing
 
 ```bash
 git clone https://github.com/getcompanion-ai/feynman.git

extensions/research-tools/alpha.ts

@@ -16,7 +16,174 @@ import type { ExtensionAPI } from "@mariozechner/pi-coding-agent";
 import { Type } from "@sinclair/typebox";
 
 import { getExtensionCommandSpec } from "../../metadata/commands.mjs";
-import { formatToolText } from "./shared.js";
+import { collapseExcessBlankLines, formatToolText } from "./shared.js";
+
+type JsonRecord = Record<string, unknown>;
+
+type AlphaSearchHit = {
+	rank?: number;
+	title?: string;
+	publishedAt?: string;
+	organizations?: string;
+	authors?: string;
+	abstract?: string;
+	arxivId?: string;
+	arxivUrl?: string;
+	alphaXivUrl?: string;
+};
+
+type AlphaSearchSection = {
+	count: number;
+	results: AlphaSearchHit[];
+	note?: string;
+};
+
+type AlphaSearchPayload = {
+	query?: string;
+	mode?: string;
+	results?: AlphaSearchHit[];
+	semantic?: AlphaSearchSection;
+	keyword?: AlphaSearchSection;
+	agentic?: AlphaSearchSection;
+};
+
+function isRecord(value: unknown): value is JsonRecord {
+	return typeof value === "object" && value !== null && !Array.isArray(value);
+}
+
+function cleanText(value: unknown, maxLength = 320): string | undefined {
+	if (typeof value !== "string") {
+		return undefined;
+	}
+
+	const collapsed = collapseExcessBlankLines(value)
+		.replace(/\s*\n\s*/g, " ")
+		.replace(/[ \t]+/g, " ");
+	if (!collapsed) {
+		return undefined;
+	}
+
+	return collapsed.length > maxLength ? `${collapsed.slice(0, maxLength - 1).trimEnd()}…` : collapsed;
+}
+
+function sanitizeHit(value: unknown, fallbackRank: number): AlphaSearchHit | null {
+	if (!isRecord(value)) {
+		return null;
+	}
+
+	const title = cleanText(value.title, 220);
+	if (!title) {
+		return null;
+	}
+
+	return {
+		rank: typeof value.rank === "number" ? value.rank : fallbackRank,
+		title,
+		publishedAt: cleanText(value.publishedAt, 48),
+		organizations: cleanText(value.organizations, 180),
+		authors: cleanText(value.authors, 220),
+		abstract: cleanText(value.abstract, 360),
+		arxivId: cleanText(value.arxivId, 32),
+		arxivUrl: cleanText(value.arxivUrl, 160),
+		alphaXivUrl: cleanText(value.alphaXivUrl, 160),
+	};
+}
+
+function sanitizeHits(value: unknown): AlphaSearchHit[] {
+	if (!Array.isArray(value)) {
+		return [];
+	}
+
+	return value
+		.map((entry, index) => sanitizeHit(entry, index + 1))
+		.filter((entry): entry is AlphaSearchHit => entry !== null);
+}
+
+function sanitizeSection(value: unknown): AlphaSearchSection {
+	if (!isRecord(value)) {
+		return { count: 0, results: [] };
+	}
+
+	const results = sanitizeHits(value.results);
+	const note = results.length === 0 ? cleanText(value.raw, 600) : undefined;
+
+	return {
+		count: results.length,
+		results,
+		...(note ? { note } : {}),
+	};
+}
+
+export function sanitizeAlphaSearchPayload(value: unknown): AlphaSearchPayload {
+	if (!isRecord(value)) {
+		return {};
+	}
+
+	const payload: AlphaSearchPayload = {
+		query: cleanText(value.query, 240),
+		mode: cleanText(value.mode, 32),
+	};
+
+	const topLevelResults = sanitizeHits(value.results);
+	if (topLevelResults.length > 0) {
+		payload.results = topLevelResults;
+	}
+
+	for (const key of ["semantic", "keyword", "agentic"] as const) {
+		if (key in value) {
+			payload[key] = sanitizeSection(value[key]);
+		}
+	}
+
+	return payload;
+}
+
+function pushHitLines(lines: string[], hit: AlphaSearchHit): void {
+	lines.push(`${hit.rank ?? "?"}. ${hit.title ?? "Untitled result"}`);
+	if (hit.arxivId) lines.push(`   arXiv: ${hit.arxivId}`);
+	if (hit.publishedAt) lines.push(`   published: ${hit.publishedAt}`);
+	if (hit.organizations) lines.push(`   orgs: ${hit.organizations}`);
+	if (hit.authors) lines.push(`   authors: ${hit.authors}`);
+	if (hit.abstract) lines.push(`   abstract: ${hit.abstract}`);
+	if (hit.arxivUrl) lines.push(`   arXiv URL: ${hit.arxivUrl}`);
+	if (hit.alphaXivUrl) lines.push(`   alphaXiv URL: ${hit.alphaXivUrl}`);
+}
+
+function pushSectionLines(lines: string[], label: string, section: AlphaSearchSection): void {
+	lines.push(`${label} (${section.count})`);
+	if (section.results.length === 0) {
+		lines.push(section.note ? `  note: ${section.note}` : "  no parsed results");
+		return;
+	}
+
+	for (const hit of section.results) {
+		pushHitLines(lines, hit);
+	}
+}
+
+export function formatAlphaSearchContext(value: unknown): string {
+	const payload = sanitizeAlphaSearchPayload(value);
+	const lines: string[] = [];
+
+	if (payload.query) lines.push(`query: ${payload.query}`);
+	if (payload.mode) lines.push(`mode: ${payload.mode}`);
+
+	if (payload.results) {
+		pushSectionLines(lines, "results", { count: payload.results.length, results: payload.results });
+	}
+
+	for (const [label, section] of [
+		["semantic", payload.semantic],
+		["keyword", payload.keyword],
+		["agentic", payload.agentic],
+	] as const) {
+		if (section) {
+			pushSectionLines(lines, label, section);
+		}
+	}
+
+	return lines.length > 0 ? lines.join("\n") : "No alpha search results returned.";
+}
 
 export function registerAlphaCommands(pi: ExtensionAPI): void {
 	pi.registerCommand("alpha-login", {
@@ -72,9 +239,10 @@ export function registerAlphaTools(pi: ExtensionAPI): void {
 		async execute(_toolCallId, params) {
 			try {
 				const result = await searchPapers(params.query, params.mode?.trim() || "all");
+				const sanitized = sanitizeAlphaSearchPayload(result);
 				return {
-					content: [{ type: "text", text: formatToolText(result) }],
-					details: result,
+					content: [{ type: "text", text: formatAlphaSearchContext(sanitized) }],
+					details: sanitized,
 				};
 			} finally {
 				await disconnect();

extensions/research-tools/shared.ts

@@ -27,8 +27,13 @@ export const FEYNMAN_RESEARCH_TOOLS = [
 	"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 {
-	return typeof result === "string" ? result : JSON.stringify(result, null, 2);
+	const text = typeof result === "string" ? result : JSON.stringify(result, null, 2);
+	return collapseExcessBlankLines(text);
 }
 
 export function getFeynmanHome(): string {

src/pi/package-presets.ts

@@ -23,13 +23,13 @@ export const OPTIONAL_PACKAGE_PRESETS = {
 	},
 } as const;
 
+export type OptionalPackagePresetName = keyof typeof OPTIONAL_PACKAGE_PRESETS;
+
 const LEGACY_DEFAULT_PACKAGE_SOURCES = [
 	...CORE_PACKAGE_SOURCES,
 	"npm:pi-generative-ui",
 ] as const;
 
-export type OptionalPackagePresetName = keyof typeof OPTIONAL_PACKAGE_PRESETS;
-
 function arraysMatchAsSets(left: readonly string[], right: readonly string[]): boolean {
 	if (left.length !== right.length) {
 		return false;

tests/alpha-tools.test.ts

@@ -0,0 +1,86 @@
+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");
+});

website/astro.config.mjs

@@ -7,8 +7,8 @@ export default defineConfig({
   markdown: {
     shikiConfig: {
       themes: {
-        light: 'github-light',
-        dark: 'github-dark',
+        light: 'everforest-light',
+        dark: 'everforest-dark',
       },
     },
   },

website/src/pages/index.astro

@@ -6,7 +6,6 @@ import AsciiLogo from '../components/AsciiLogo.astro';
 <Base title="Feynman — The open source AI research agent" active="home">
   <section class="text-center pt-24 pb-20 px-6">
     <div class="max-w-2xl mx-auto">
-      <AsciiLogo size="hero" class="mb-4" />
       <h1 class="text-5xl sm:text-6xl font-bold tracking-tight mb-6" style="text-wrap: balance">The open source AI research agent</h1>
       <p class="text-lg text-text-muted mb-10 leading-relaxed" style="text-wrap: pretty">Investigate topics, write papers, run experiments, review research, audit codebases &mdash; every output cited and source-grounded</p>
       <button id="copy-btn" class="group inline-flex items-center justify-between gap-3 bg-surface rounded-lg px-5 py-3 mb-8 font-mono text-sm hover:border-accent/40 hover:text-accent transition-colors focus-visible:outline-none focus-visible:ring-2 focus-visible:ring-accent rounded-lg border border-border max-w-full" aria-label="Copy install command">
@@ -20,6 +19,9 @@ import AsciiLogo from '../components/AsciiLogo.astro';
         <a href="https://github.com/getcompanion-ai/feynman" target="_blank" rel="noopener" class="px-6 py-2.5 rounded-lg border border-border text-text-muted font-semibold text-sm hover:border-text-dim hover:text-text-primary transition-colors focus-visible:outline-none focus-visible:ring-2 focus-visible:ring-accent focus-visible:ring-offset-2 focus-visible:ring-offset-bg">GitHub</a>
       </div>
     </div>
+    <div class="max-w-4xl mx-auto mt-16">
+      <img src="/hero-raw.png" alt="Feynman CLI" class="w-full" />
+    </div>
   </section>
 
   <section class="py-20 px-6">

website/src/styles/global.css

@@ -3,31 +3,31 @@
 @tailwind utilities;
 
 :root {
-  --color-bg: #f0f5f1;
-  --color-surface: #e4ece6;
-  --color-surface-2: #d8e3db;
-  --color-border: #c2d1c6;
-  --color-text: #1a2e22;
-  --color-text-muted: #3d5c4a;
-  --color-text-dim: #6b8f7a;
-  --color-accent: #0d9668;
-  --color-accent-hover: #077a54;
-  --color-accent-subtle: #c6e4d4;
-  --color-teal: #0e8a7d;
+  --color-bg: #f3ead3;
+  --color-surface: #eae4ca;
+  --color-surface-2: #e0dbc2;
+  --color-border: #c9c4b0;
+  --color-text: #3a464c;
+  --color-text-muted: #5c6a72;
+  --color-text-dim: #859289;
+  --color-accent: #6e8b53;
+  --color-accent-hover: #5a7342;
+  --color-accent-subtle: #d5e3bf;
+  --color-teal: #5da09a;
 }
 
 .dark {
-  --color-bg: #050a08;
-  --color-surface: #0c1410;
-  --color-surface-2: #131f1a;
-  --color-border: #1b2f26;
-  --color-text: #f0f5f2;
-  --color-text-muted: #8aaa9a;
-  --color-text-dim: #4d7565;
-  --color-accent: #34d399;
-  --color-accent-hover: #10b981;
-  --color-accent-subtle: #064e3b;
-  --color-teal: #2dd4bf;
+  --color-bg: #2d353b;
+  --color-surface: #343f44;
+  --color-surface-2: #3a464c;
+  --color-border: #5c6a72;
+  --color-text: #d3c6aa;
+  --color-text-muted: #9da9a0;
+  --color-text-dim: #859289;
+  --color-accent: #a7c080;
+  --color-accent-hover: #93ad6c;
+  --color-accent-subtle: #425047;
+  --color-teal: #7fbbb3;
 }
 
 html {
@@ -87,7 +87,7 @@ body {
 .prose code {
   font-family: 'SF Mono', 'Fira Code', 'JetBrains Mono', monospace;
   font-size: 0.875rem;
-  background-color: var(--color-surface);
+  background-color: var(--color-surface-2);
   padding: 0.125rem 0.375rem;
   border-radius: 0.25rem;
   color: var(--color-text);
@@ -95,7 +95,6 @@ body {
 
 .prose pre {
   position: relative;
-  background-color: var(--color-surface) !important;
   border-radius: 0.5rem;
   padding: 1rem 1.25rem;
   overflow-x: auto;
@@ -103,13 +102,13 @@ body {
   font-family: 'SF Mono', 'Fira Code', 'JetBrains Mono', monospace;
   font-size: 0.875rem;
   line-height: 1.7;
+  border: 1px solid var(--color-border);
 }
 
 .prose pre code {
   background: none !important;
   border: none;
   padding: 0;
-  color: var(--color-text);
 }
 
 .copy-code {
@@ -137,9 +136,6 @@ pre:hover .copy-code {
   color: var(--color-accent);
 }
 
-.prose pre code span {
-  color: inherit !important;
-}
 
 .prose table {
   width: 100%;
@@ -201,6 +197,34 @@ pre:hover .copy-code {
   margin-bottom: 1rem;
 }
 
+* {
+  scrollbar-width: thin;
+  scrollbar-color: var(--color-border) transparent;
+}
+
+::-webkit-scrollbar {
+  width: 8px;
+  height: 8px;
+}
+
+::-webkit-scrollbar-track {
+  background: transparent;
+}
+
+::-webkit-scrollbar-thumb {
+  background: var(--color-border);
+  border-radius: 4px;
+}
+
+::-webkit-scrollbar-thumb:hover {
+  background: var(--color-text-dim);
+}
+
+::selection {
+  background: var(--color-accent-subtle);
+  color: var(--color-text);
+}
+
 .agent-entry {
   background-color: var(--color-surface);
   border-radius: 0.75rem;