Add plan-confirm steps to all workflows, cite alphaXiv and Agent Computer, add visuals to writer

- Every workflow prompt now shows a plan and asks the user to confirm before executing
- /autoresearch asks for execution environment (local, branch, venv, cloud) and confirms before looping
- Writer agent and key prompts now generate charts (pi-charts) and diagrams (Mermaid) when data calls for it
- Cite alphaXiv and Agent Computer in README and website homepage
- Clear terminal screen before launching Pi TUI
- Remove Alpha Hub GitHub link in favor of alphaxiv.org

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

.feynman/agents/writer.md

@@ -32,6 +32,13 @@ Detailed findings organized by theme or question.
 Unresolved issues, disagreements between sources, gaps in evidence.
 ```
 
+## Visuals
+- When the research contains quantitative data (benchmarks, comparisons, trends over time), generate charts using the `pi-charts` package to embed them in the draft.
+- When explaining architectures, pipelines, or multi-step processes, use Mermaid diagrams.
+- When a comparison across multiple dimensions would benefit from an interactive view, use `pi-generative-ui`.
+- Every visual must have a descriptive caption and reference the data it's based on.
+- Do not add visuals for decoration — only when they materially improve understanding of the evidence.
+
 ## Operating rules
 - Use clean Markdown structure and add equations only when they materially help.
 - Keep the narrative readable, but never outrun the evidence.

README.md

@@ -58,6 +58,7 @@ Four bundled research agents, dispatched automatically or via subagent commands.
 ## Tools
 
 - **[AlphaXiv](https://www.alphaxiv.org/)** — paper search, Q&A, code reading, persistent annotations
+- **[Agent Computer](https://agentcomputer.ai)** — secure cloud execution for experiments, replications, and long-running research
 - **Web search** — Gemini or Perplexity, zero-config default via signed-in Chromium
 - **Session search** — indexed recall across prior research sessions
 - **Preview** — browser and PDF export of generated artifacts
@@ -81,7 +82,7 @@ feynman search status               # web search config
 
 ## How it works
 
-Built on [Pi](https://github.com/mariozechner/pi-coding-agent) and [Alpha Hub](https://github.com/getcompanion-ai/alpha-hub). Pi provides the agent runtime — file access, shell execution, persistent sessions, custom extensions. Alpha Hub connects to [alphaXiv](https://www.alphaxiv.org/) for paper search, Q&A, code reading, and annotations.
+Built on [Pi](https://github.com/mariozechner/pi-coding-agent), [alphaXiv](https://www.alphaxiv.org/), and [Agent Computer](https://agentcomputer.ai). Pi provides the agent runtime. alphaXiv powers paper search, Q&A, code reading, and annotations. Agent Computer provides secure cloud machines for running experiments and replications.
 
 Every output is source-grounded. Claims link to papers, docs, or repos with direct URLs.
 
@@ -96,4 +97,4 @@ cd feynman && npm install && npm run start
 
 [Docs](https://feynman.companion.ai/docs) · [MIT License](LICENSE)
 
-Built on [Pi](https://github.com/mariozechner/pi-coding-agent) and [Alpha Hub](https://github.com/getcompanion-ai/alpha-hub).
+Built on [Pi](https://github.com/mariozechner/pi-coding-agent), [alphaXiv](https://www.alphaxiv.org/), and [Agent Computer](https://agentcomputer.ai).

prompts/audit.md

@@ -7,6 +7,7 @@ topLevelCli: true
 Audit the paper and codebase for: $@
 
 Requirements:
+- Before starting, outline the audit plan: which paper, which repo, which claims to check. Present the plan to the user and confirm before proceeding.
 - Use the `researcher` subagent for evidence gathering and the `verifier` subagent to verify sources and add inline citations when the audit is non-trivial.
 - Compare claimed methods, defaults, metrics, and data handling against the actual code.
 - Call out missing code, mismatches, ambiguous defaults, and reproduction risks.

prompts/autoresearch.md

@@ -6,19 +6,46 @@ topLevelCli: true
 ---
 Start an autoresearch optimization loop for: $@
 
-This command uses pi-autoresearch. Enter autoresearch mode and begin the autonomous experiment loop.
+This command uses pi-autoresearch.
 
-## Behavior
+## Step 1: Gather
 
-- If `autoresearch.md` and `autoresearch.jsonl` already exist in the project, resume the existing session with the user's input as additional context.
+If `autoresearch.md` and `autoresearch.jsonl` already exist, ask the user if they want to resume or start fresh.
-- Otherwise, gather the optimization target from the user:
-  - What to optimize (test speed, bundle size, training loss, build time, etc.)
-  - The benchmark command to run
-  - The metric name, unit, and direction (lower/higher is better)
-  - Files in scope for changes
-- Then initialize the session: create `autoresearch.md`, `autoresearch.sh`, run the baseline, and start looping.
 
-## Loop
+Otherwise, collect the following from the user before doing anything else:
+- What to optimize (test speed, bundle size, training loss, build time, etc.)
+- The benchmark command to run
+- The metric name, unit, and direction (lower/higher is better)
+- Files in scope for changes
+- Maximum number of iterations (default: 20)
+
+## Step 2: Environment
+
+Ask the user where to run:
+- **Local** — run in the current working directory
+- **New git branch** — create a branch so main stays clean
+- **Virtual environment** — create an isolated venv/conda env first
+- **Cloud** — delegate to a remote Agent Computer machine via `/delegate`
+
+Do not proceed without a clear answer.
+
+## Step 3: Confirm
+
+Present the full plan to the user before starting:
+
+```
+Optimization target: [metric] ([direction])
+Benchmark command:   [command]
+Files in scope:      [files]
+Environment:         [chosen environment]
+Max iterations:      [N]
+```
+
+Ask the user to confirm. Do not start the loop without explicit approval.
+
+## Step 4: Run
+
+Initialize the session: create `autoresearch.md`, `autoresearch.sh`, run the baseline, and start looping.
 
 Each iteration: edit → commit → `run_experiment` → `log_experiment` → keep or revert → repeat. Do not stop unless interrupted or `maxIterations` is reached.
 

prompts/compare.md

@@ -7,8 +7,10 @@ topLevelCli: true
 Compare sources for: $@
 
 Requirements:
+- Before starting, outline the comparison plan: which sources to compare, which dimensions to evaluate, expected output structure. Present the plan to the user and confirm before proceeding.
 - Use the `researcher` subagent to gather source material when the comparison set is broad, and the `verifier` subagent to verify sources and add inline citations to the final matrix.
 - Build a comparison matrix covering: source, key claim, evidence type, caveats, confidence.
+- Generate charts with `pi-charts` when the comparison involves quantitative metrics. Use Mermaid for method or architecture comparisons.
 - Distinguish agreement, disagreement, and uncertainty clearly.
 - Save exactly one comparison to `outputs/` as markdown.
 - End with a `Sources` section containing direct URLs for every source used.

prompts/deepresearch.md

@@ -40,6 +40,8 @@ Write the plan to `outputs/.plans/deepresearch-plan.md` as a self-contained arti
 
 Also save the plan with `memory_remember` (type: `fact`, key: `deepresearch.plan`) so it survives context truncation.
 
+Present the plan to the user and ask them to confirm before proceeding. If the user wants changes, revise the plan first.
+
 ## 2. Scale decision
 
 | Query type | Execution |
@@ -107,6 +109,8 @@ Detailed findings organized by theme or question.
 Unresolved issues, disagreements between sources, gaps in evidence.
 ```
 
+When the research includes quantitative data (benchmarks, performance comparisons, trends), generate charts using `pi-charts`. Use Mermaid diagrams for architectures and processes. Every visual must have a caption and reference the underlying data.
+
 Save this draft to a temp file (e.g., `draft.md` in the chain artifacts dir or a temp path).
 
 ## 6. Cite

prompts/draft.md

@@ -7,8 +7,10 @@ topLevelCli: true
 Write a paper-style draft for: $@
 
 Requirements:
+- Before writing, outline the draft structure: proposed title, sections, key claims to make, and source material to draw from. Present the outline to the user and confirm before proceeding.
 - Use the `writer` subagent when the draft should be produced from already-collected notes, then use the `verifier` subagent to add inline citations and verify sources.
 - Include at minimum: title, abstract, problem statement, related work, method or synthesis, evidence or experiments, limitations, conclusion.
 - Use clean Markdown with LaTeX where equations materially help.
+- Generate charts with `pi-charts` for quantitative data, benchmarks, and comparisons. Use Mermaid for architectures and pipelines. Every figure needs a caption.
 - Save exactly one draft to `papers/` as markdown.
 - End with a `Sources` appendix with direct URLs for all primary references.

prompts/lit.md

@@ -8,8 +8,9 @@ Investigate the following topic as a literature review: $@
 
 ## Workflow
 
-1. **Gather** — Use the `researcher` subagent when the sweep is wide enough to benefit from delegated paper triage before synthesis. For narrow topics, search directly.
+1. **Plan** — Outline the scope: key questions, source types to search (papers, web, repos), time period, and expected sections. Present the plan to the user and confirm before proceeding.
-2. **Synthesize** — Separate consensus, disagreements, and open questions. When useful, propose concrete next experiments or follow-up reading.
+2. **Gather** — Use the `researcher` subagent when the sweep is wide enough to benefit from delegated paper triage before synthesis. For narrow topics, search directly.
-3. **Cite** — Spawn the `verifier` agent to add inline citations and verify every source URL in the draft.
+2. **Synthesize** — Separate consensus, disagreements, and open questions. When useful, propose concrete next experiments or follow-up reading. Generate charts with `pi-charts` for quantitative comparisons across papers and Mermaid diagrams for taxonomies or method pipelines.
-4. **Verify** — Spawn the `reviewer` agent to check the cited draft for unsupported claims, logical gaps, and single-source critical findings. Fix FATAL issues before delivering. Note MAJOR issues in Open Questions.
+4. **Cite** — Spawn the `verifier` agent to add inline citations and verify every source URL in the draft.
-5. **Deliver** — Save exactly one literature review to `outputs/` as markdown. Write a provenance record alongside it as `<filename>.provenance.md` listing: date, sources consulted vs. accepted vs. rejected, verification status, and intermediate research files used.
+5. **Verify** — Spawn the `reviewer` agent to check the cited draft for unsupported claims, logical gaps, and single-source critical findings. Fix FATAL issues before delivering. Note MAJOR issues in Open Questions.
+6. **Deliver** — Save exactly one literature review to `outputs/` as markdown. Write a provenance record alongside it as `<filename>.provenance.md` listing: date, sources consulted vs. accepted vs. rejected, verification status, and intermediate research files used.

prompts/review.md

@@ -7,6 +7,7 @@ topLevelCli: true
 Review this AI research artifact: $@
 
 Requirements:
+- Before starting, outline what will be reviewed and the review criteria (novelty, empirical rigor, baselines, reproducibility, etc.). Present the plan to the user and confirm before proceeding.
 - Spawn a `researcher` subagent to gather evidence on the artifact — inspect the paper, code, cited work, and any linked experimental artifacts. Save to `research.md`.
 - Spawn a `reviewer` subagent with `research.md` to produce the final peer review with inline annotations.
 - For small or simple artifacts where evidence gathering is overkill, run the `reviewer` subagent directly instead.

prompts/watch.md

@@ -7,8 +7,8 @@ topLevelCli: true
 Create a research watch for: $@
 
 Requirements:
+- Before starting, outline the watch plan: what to monitor, what signals matter, what counts as a meaningful change, and the check frequency. Present the plan to the user and confirm before proceeding.
 - Start with a baseline sweep of the topic.
-- Summarize what should be monitored, what signals matter, and what counts as a meaningful change.
 - Use `schedule_prompt` to create the recurring or delayed follow-up instead of merely promising to check later.
 - Save exactly one baseline artifact to `outputs/`.
 - End with a `Sources` section containing direct URLs for every source used.

src/pi/launch.ts

@@ -12,6 +12,10 @@ export async function launchPiChat(options: PiRuntimeOptions): Promise<void> {
 		throw new Error(`Promise polyfill not found: ${promisePolyfillPath}`);
 	}
 
+	if (process.stdout.isTTY) {
+		process.stdout.write("\x1b[2J\x1b[3J\x1b[H");
+	}
+
 	const child = spawn(process.execPath, ["--import", promisePolyfillPath, piCliPath, ...buildPiArgs(options)], {
 		cwd: options.workingDir,
 		stdio: "inherit",

website/src/pages/index.astro

@@ -111,11 +111,15 @@ import Base from '../layouts/Base.astro';
   <section class="py-20 px-6">
     <div class="max-w-5xl mx-auto">
       <h2 class="text-2xl font-bold text-center mb-12">Tools</h2>
-      <div class="grid grid-cols-1 sm:grid-cols-2 gap-4 max-w-2xl mx-auto">
+      <div class="grid grid-cols-1 sm:grid-cols-2 gap-4 max-w-3xl mx-auto">
         <div class="bg-surface rounded-xl p-5">
-          <div class="font-semibold mb-1">AlphaXiv</div>
+          <div class="font-semibold mb-1"><a href="https://www.alphaxiv.org/" class="text-accent hover:underline">AlphaXiv</a></div>
           <p class="text-sm text-text-muted">Paper search, Q&A, code reading, persistent annotations</p>
         </div>
+        <div class="bg-surface rounded-xl p-5">
+          <div class="font-semibold mb-1"><a href="https://agentcomputer.ai" class="text-accent hover:underline">Agent Computer</a></div>
+          <p class="text-sm text-text-muted">Secure cloud execution for experiments and replications</p>
+        </div>
         <div class="bg-surface rounded-xl p-5">
           <div class="font-semibold mb-1">Web search</div>
           <p class="text-sm text-text-muted">Gemini or Perplexity, zero-config default</p>
@@ -134,7 +138,7 @@ import Base from '../layouts/Base.astro';
 
   <section class="py-20 px-6 text-center">
     <div class="max-w-xl mx-auto">
-      <p class="text-text-muted mb-6">Built on <a href="https://github.com/mariozechner/pi-coding-agent" class="text-accent hover:underline">Pi</a> and <a href="https://github.com/getcompanion-ai/alpha-hub" class="text-accent hover:underline">Alpha Hub</a>. MIT licensed. Open source.</p>
+      <p class="text-text-muted mb-6">Built on <a href="https://github.com/mariozechner/pi-coding-agent" class="text-accent hover:underline">Pi</a>, <a href="https://www.alphaxiv.org/" class="text-accent hover:underline">alphaXiv</a>, and <a href="https://agentcomputer.ai" class="text-accent hover:underline">Agent Computer</a>. MIT licensed. Open source.</p>
       <div class="flex gap-4 justify-center flex-wrap">
         <a href="/docs/getting-started/installation" class="px-6 py-2.5 rounded-lg bg-accent text-bg font-semibold text-sm hover:bg-accent-hover transition-colors">Get started</a>
         <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">GitHub</a>