chore: remove the persistent /agents-panel; keep /agents overlay and live widget

CHANGELOG.md

@@ -43,14 +43,6 @@
   tree glyphs (├─/└─/│), colored statuses and icons, live elapsed time,
   keyboard navigation (↑/↓), and a detail pane (Enter) showing each agent's
   task and result. The live widget header now hints at `/agents`.
-- New `/agents-panel` command toggles a persistent OpenCode-style right-side
-  panel with the live agent tree: non-capturing (typing keeps working),
-  auto-refreshed every 1.5 s, hidden on terminals narrower than 100 columns,
-  and closed automatically on shutdown.
-- The right-side panel now fills the whole right column (width 40%, full
-  height) and shows each running subagent's most recent activity under its
-  row — the last tool call with its query or the last assistant text — read
-  from the tail of the agent's session file (cached by file size).
 
 ## 0.1.1 — 2026-07-31
 

graphify-out/.graphify_labels.json

@@ -0,0 +1,23 @@
+{
+  "0": "Community 0",
+  "1": "Community 1",
+  "2": "Community 2",
+  "3": "Community 3",
+  "4": "Community 4",
+  "5": "Community 5",
+  "6": "Community 6",
+  "8": "Community 8",
+  "9": "Community 9",
+  "10": "Community 10",
+  "11": "Community 11",
+  "12": "Community 12",
+  "13": "Community 13",
+  "14": "Community 14",
+  "15": "Community 15",
+  "16": "Community 16",
+  "17": "Community 17",
+  "18": "Community 18",
+  "19": "Community 19",
+  "20": "Community 20",
+  "21": "Community 21"
+}

graphify-out/.graphify_root

@@ -0,0 +1 @@
+.

graphify-out/GRAPH_REPORT.md

@@ -0,0 +1,141 @@
+# Graph Report - hypothesis-machine  (2026-08-01)
+
+## Corpus Check
+- 45 files · ~18,068 words
+- Verdict: corpus is large enough that graph structure adds value.
+
+## Summary
+- 331 nodes · 619 edges · 21 communities (14 shown, 7 thin omitted)
+- Extraction: 100% EXTRACTED · 0% INFERRED · 0% AMBIGUOUS
+- Token cost: 0 input · 0 output
+
+## Graph Freshness
+- Built from commit: `8f308ece`
+- Run `git rev-parse HEAD` and compare to check if the graph is stale.
+- Run `graphify update .` after code changes (no API cost).
+
+## Community Hubs (Navigation)
+- [[_COMMUNITY_Community 0|Community 0]]
+- [[_COMMUNITY_Community 1|Community 1]]
+- [[_COMMUNITY_Community 2|Community 2]]
+- [[_COMMUNITY_Community 3|Community 3]]
+- [[_COMMUNITY_Community 4|Community 4]]
+- [[_COMMUNITY_Community 5|Community 5]]
+- [[_COMMUNITY_Community 6|Community 6]]
+- [[_COMMUNITY_Community 8|Community 8]]
+- [[_COMMUNITY_Community 9|Community 9]]
+- [[_COMMUNITY_Community 10|Community 10]]
+- [[_COMMUNITY_Community 11|Community 11]]
+- [[_COMMUNITY_Community 12|Community 12]]
+- [[_COMMUNITY_Community 13|Community 13]]
+- [[_COMMUNITY_Community 14|Community 14]]
+- [[_COMMUNITY_Community 15|Community 15]]
+- [[_COMMUNITY_Community 16|Community 16]]
+- [[_COMMUNITY_Community 17|Community 17]]
+- [[_COMMUNITY_Community 18|Community 18]]
+- [[_COMMUNITY_Community 19|Community 19]]
+- [[_COMMUNITY_Community 20|Community 20]]
+
+## God Nodes (most connected - your core abstractions)
+1. `AgentTree` - 44 edges
+2. `ResearchMemory` - 22 edges
+3. `SupervisorIntegration` - 22 edges
+4. `RunStore` - 21 edges
+5. `WebGateway` - 18 edges
+6. `AgentRecord` - 18 edges
+7. `ResearchLoop` - 14 edges
+8. `ExperimentRunner` - 14 edges
+9. `compilerOptions` - 13 edges
+10. `HypothesisMachineConfig` - 10 edges
+
+## Surprising Connections (you probably didn't know these)
+- `FakeRuntime` --implements--> `AgentRuntime`  [EXTRACTED]
+  tests/helpers.ts → src/types.ts
+- `TreeRow` --references--> `AgentRecord`  [EXTRACTED]
+  src/agent-tree-ui.ts → src/types.ts
+- `FakeRuntimeFactory` --implements--> `AgentRuntimeFactory`  [EXTRACTED]
+  tests/helpers.ts → src/types.ts
+- `AgentTree` --references--> `AgentFactory`  [EXTRACTED]
+  src/agent-tree.ts → src/agent-factory.ts
+- `AgentTree` --references--> `RunManifest`  [EXTRACTED]
+  src/agent-tree.ts → src/run-store.ts
+
+## Import Cycles
+- None detected.
+
+## Communities (21 total, 7 thin omitted)
+
+### Community 0 - "Community 0"
+Cohesion: 0.06
+Nodes (34): DEFAULT_CONFIG, HypothesisMachineConfig, loadConfig(), hypothesisMachine(), PiRuntimeDependencies, frontmatterDocument(), MEMORY_STATUSES, MEMORY_TYPES (+26 more)
+
+### Community 1 - "Community 1"
+Cohesion: 0.12
+Nodes (3): AgentTree, PiAgentRuntimeFactory, AgentResult
+
+### Community 2 - "Community 2"
+Cohesion: 0.07
+Nodes (25): Browser Use adapter contract, Contributing, Local setup, Pull requests, Architecture, Development, Assumptions corrected after verification, Implemented here (+17 more)
+
+### Community 3 - "Community 3"
+Cohesion: 0.06
+Nodes (33): dependencies, @earendil-works/pi-agent-core, @earendil-works/pi-ai, @earendil-works/pi-coding-agent, @earendil-works/pi-tui, typebox, yaml, description (+25 more)
+
+### Community 4 - "Community 4"
+Cohesion: 0.18
+Nodes (8): activityCache, agentLastActivity(), collapse(), createAgentPanelComponent(), createAgentTreeOverlay(), STATUS_COLOR, STATUS_ICON, TreeRow
+
+### Community 6 - "Community 6"
+Cohesion: 0.12
+Nodes (15): AgentFactory, taskFingerprint(), AgentTreeError, TreeOptions, RunManifest, RunStore, AgentRecord, AgentRuntime (+7 more)
+
+### Community 8 - "Community 8"
+Cohesion: 0.27
+Nodes (9): AgentSpecError, ALLOWED_TOOLS, parseAgentSpec(), readAgentSpec(), REQUIRED_SECTIONS, section(), serializeAgentSpec(), writeAgentSpec() (+1 more)
+
+### Community 9 - "Community 9"
+Cohesion: 0.22
+Nodes (4): IterationReport, LoopStatus, ResearchLoop, ResearchLoopState
+
+### Community 11 - "Community 11"
+Cohesion: 0.13
+Nodes (14): compilerOptions, esModuleInterop, exactOptionalPropertyTypes, module, moduleResolution, noUncheckedIndexedAccess, outDir, resolveJsonModule (+6 more)
+
+### Community 13 - "Community 13"
+Cohesion: 0.25
+Nodes (7): compilerOptions, declaration, outDir, rootDir, exclude, extends, include
+
+### Community 14 - "Community 14"
+Cohesion: 0.40
+Nodes (4): 0.1.0 — 2026-07-31, 0.1.1 — 2026-07-31, Changelog, Unreleased
+
+### Community 15 - "Community 15"
+Cohesion: 0.50
+Nodes (3): Security and data, Summary, Verification
+
+### Community 16 - "Community 16"
+Cohesion: 0.50
+Nodes (3): child, commands, responses
+
+## Knowledge Gaps
+- **105 isolated node(s):** `name`, `version`, `description`, `keywords`, `type` (+100 more)
+  These have ≤1 connection - possible missing edges or undocumented components.
+- **7 thin communities (<3 nodes) omitted from report** — run `graphify query` to explore isolated nodes.
+
+## Suggested Questions
+_Questions this graph is uniquely positioned to answer:_
+
+- **Why does `AgentTree` connect `Community 1` to `Community 0`, `Community 10`, `Community 4`, `Community 6`?**
+  _High betweenness centrality (0.107) - this node is a cross-community bridge._
+- **Why does `SupervisorIntegration` connect `Community 10` to `Community 0`, `Community 1`, `Community 9`?**
+  _High betweenness centrality (0.063) - this node is a cross-community bridge._
+- **Why does `ResearchMemory` connect `Community 0` to `Community 10`?**
+  _High betweenness centrality (0.045) - this node is a cross-community bridge._
+- **What connects `name`, `version`, `description` to the rest of the system?**
+  _105 weakly-connected nodes found - possible documentation gaps or missing edges._
+- **Should `Community 0` be split into smaller, more focused modules?**
+  _Cohesion score 0.058596491228070174 - nodes in this community are weakly interconnected._
+- **Should `Community 1` be split into smaller, more focused modules?**
+  _Cohesion score 0.11942959001782531 - nodes in this community are weakly interconnected._
+- **Should `Community 2` be split into smaller, more focused modules?**
+  _Cohesion score 0.0677361853832442 - nodes in this community are weakly interconnected._

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+  },
+  "docs/pi-capabilities.md": {
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+  "docs/releasing.md": {
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+  "docs/security.md": {
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+    "ast_hash": "d1a39881546c3c2a6c80008cf59c3483",
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+    "ast_hash": "d5264ae5950629e067955aa66cbba7f4",
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+    "ast_hash": "4d89744864f680a763838d70ff9c8a7c",
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+  "services/browser-worker/README.md": {
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+}

src/agent-tree-ui.ts

@@ -1,5 +1,4 @@
 import { Key, matchesKey, truncateToWidth, wrapTextWithAnsi } from "@earendil-works/pi-tui";
-import { closeSync, openSync, readSync, statSync } from "node:fs";
 import type { Theme } from "@earendil-works/pi-coding-agent";
 import type { AgentTree } from "./agent-tree.js";
 import type { AgentRecord } from "./types.js";
@@ -45,79 +44,6 @@ function elapsed(record: AgentRecord, now: number): string {
   return `${String(Math.floor(span / 60)).padStart(2, "0")}:${String(span % 60).padStart(2, "0")}`;
 }
 
-/** Cache of the last observed session-file size and its extracted activity line. */
-const activityCache = new Map<string, { size: number; line: string }>();
-
-function collapse(text: string): string { return text.replace(/\s+/g, " ").trim(); }
-
-/** Read the tail of an agent session file and extract its most recent activity: last tool call (name + query) or last assistant text. */
-export function agentLastActivity(sessionFile: string | undefined): string | undefined {
-  if (!sessionFile) return undefined;
-  let size: number;
-  try { size = statSync(sessionFile).size; } catch { return undefined; }
-  const cached = activityCache.get(sessionFile);
-  if (cached && cached.size === size) return cached.line || undefined;
-  let text = "";
-  try {
-    const fd = openSync(sessionFile, "r");
-    try { const start = Math.max(0, size - 65536); const buf = Buffer.alloc(size - start); readSync(fd, buf, 0, buf.length, start); text = buf.toString("utf8"); } finally { closeSync(fd); }
-  } catch { return cached?.line || undefined; }
-  const queries = new Map<string, string | undefined>();
-  let toolName: string | undefined; let toolId: string | undefined; let lastText: string | undefined;
-  for (const raw of text.split("\n")) {
-    let entry: { message?: { role?: string; toolName?: string; toolCallId?: string; content?: Array<{ type?: string; id?: string; name?: string; arguments?: unknown; text?: string }> } };
-    try { entry = JSON.parse(raw) as typeof entry; } catch { continue; }
-    const msg = entry?.message; if (!msg) continue;
-    if (msg.role === "toolResult") { toolName = msg.toolName; toolId = msg.toolCallId; }
-    if (msg.role === "assistant" && Array.isArray(msg.content)) {
-      for (const part of msg.content) {
-        if (part?.type === "toolCall" && typeof part.id === "string") {
-          const args = part.arguments as Record<string, unknown> | undefined;
-          const query = typeof args?.query === "string" ? args.query : args ? String(Object.values(args)[0] ?? "") : "";
-          queries.set(part.id, query);
-        }
-        if (part?.type === "text" && typeof part.text === "string" && part.text.trim()) lastText = collapse(part.text);
-      }
-    }
-  }
-  const line = toolName ? ` ${toolName}${toolId && queries.get(toolId) ? `: \"${queries.get(toolId)}\"` : ""}` : lastText ? ` ${lastText}` : "";
-  activityCache.set(sessionFile, { size, line });
-  return line || undefined;
-}
-
-/** Persistent non-capturing right-side panel: live agent tree without keyboard navigation. */
-export function createAgentPanelComponent(
-  tree: AgentTree,
-  tui: { requestRender(): void },
-  theme: Theme,
-  done: () => void,
-): { render(width: number): string[]; invalidate(): void; handleInput(data: string): void; dispose(): void } {
-  const timer = setInterval(() => tui.requestRender(), 1500);
-  return {
-    render(width) {
-      const rows = buildRows(tree).filter((row) => row.depth > 0);
-      const now = Date.now();
-      const active = rows.filter((row) => row.record.status === "running" || row.record.status === "waiting").length;
-      const lines: string[] = [theme.fg("accent", `◆ agents`) + theme.fg("dim", ` · ${tree.runId}`), theme.fg("dim", `${active} active · ${rows.length} agents`), ""];
-      for (const { record, prefix } of rows) {
-        const icon = STATUS_ICON[record.status];
-        const status = STATUS_COLOR[record.status](theme, record.status);
-        const time = elapsed(record, now);
-        lines.push(`${prefix}${theme.fg("text", icon)} ${theme.fg("text", shortName(record.id))} ${status}${time ? ` ${theme.fg("dim", time)}` : ""}`);
-        if (record.status === "running" || record.status === "waiting") {
-          const activity = agentLastActivity(record.sessionFile);
-          if (activity) lines.push(theme.fg("dim", `  ${truncateToWidth(activity, Math.max(20, width - 8))}`));
-        }
-      }
-      lines.push("", theme.fg("dim", "/agents — details · /agents-panel — hide"));
-      return lines.map((line) => truncateToWidth(line, width));
-    },
-    invalidate() { /* rebuilt fresh on every render */ },
-    handleInput() { /* non-capturing: keys go to the editor */ },
-    dispose() { clearInterval(timer); },
-  };
-}
-
 /** Interactive overlay showing the full agent tree with live statuses, keyboard navigation, and a detail pane. */
 export function createAgentTreeOverlay(
   tree: AgentTree,

src/index.ts

@@ -12,7 +12,6 @@ export default function hypothesisMachine(pi: ExtensionAPI): void {
 
   pi.registerCommand("team", { description: "Show the recursive research team", handler: async (_args, ctx) => { ctx.ui.notify(supervisor.team(), "info"); } });
   pi.registerCommand("agents", { description: "Show the interactive agent tree overlay", handler: async (_args, ctx) => { await supervisor.showAgentTree(ctx); } });
-  pi.registerCommand("agents-panel", { description: "Toggle a persistent right-side agent panel", handler: async (_args, ctx) => { if (supervisor.agentPanelClose) { supervisor.agentPanelClose(); ctx.ui.notify("Agent panel closed", "info"); return; } if (!supervisor.tree) { ctx.ui.notify("Hypothesis Machine is not initialized", "warning"); return; } void supervisor.showAgentPanel(ctx); ctx.ui.notify("Agent panel opened (needs a wide terminal)", "info"); } });
   pi.registerCommand("research", { description: "Start a bounded research run", handler: async (args, ctx) => { const goal = args.trim(); if (!goal) { ctx.ui.notify("Usage: /research <goal>", "warning"); return; } const state = supervisor.loop; if (!state || !supervisor.tree) throw new Error("Not initialized"); supervisor.tree.setGoal(goal); state.setGoal(goal); state.start(); const prompt = `Research goal: ${goal}\nUse research_control and the recursive agent tools. Create specialized children only when useful. Record each iteration and stop on the coded conditions. Report important progress without flooding the chat.`; if (ctx.isIdle()) pi.sendUserMessage(prompt); else pi.sendUserMessage(prompt, { deliverAs: "followUp" }); } });
   pi.registerCommand("research-status", { description: "Show research loop state", handler: async (_args, ctx) => { ctx.ui.notify(JSON.stringify(supervisor.loop?.snapshot() ?? {}, null, 2), "info"); } });
   pi.registerCommand("research-pause", { description: "Pause spawning and the loop", handler: async (_args, ctx) => { if (supervisor.loop?.snapshot().status !== "running") { ctx.ui.notify("Cannot pause a non-running loop", "warning"); return; } supervisor.loop?.pause(); supervisor.tree?.pause(); ctx.ui.notify("Research paused", "info"); } });

src/supervisor.ts

@@ -1,7 +1,7 @@
 import { resolve } from "node:path";
 import { defineTool, ModelRuntime, type ExtensionAPI, type ExtensionContext, type ModelRegistry, type Theme, type ToolDefinition } from "@earendil-works/pi-coding-agent";
 import { Text, truncateToWidth } from "@earendil-works/pi-tui";
-import { createAgentPanelComponent, createAgentTreeOverlay } from "./agent-tree-ui.js";
+import { createAgentTreeOverlay } from "./agent-tree-ui.js";
 import { Type } from "typebox";
 import { StringEnum } from "@earendil-works/pi-ai";
 import { AgentTree } from "./agent-tree.js";
@@ -24,8 +24,6 @@ export class SupervisorIntegration {
   private lastScheduledIteration = 0;
   private widgetTimer: NodeJS.Timeout | undefined;
   private requestAgentRender: (() => void) | undefined;
-  /** Closes the persistent right-side agent panel if it is open. */
-  agentPanelClose: (() => void) | undefined;
   constructor(private readonly pi: ExtensionAPI) {}
 
   async start(ctx: ExtensionContext): Promise<void> {
@@ -75,18 +73,6 @@ export class SupervisorIntegration {
     });
   }
 
-  /** Open a persistent non-capturing agent panel on the right side (OpenCode-style). */
-  async showAgentPanel(ctx: ExtensionContext): Promise<void> {
-    const tree = this.required().tree;
-    await ctx.ui.custom<undefined>((tui, theme, _kb, done) => {
-      this.agentPanelClose = () => done(undefined);
-      return createAgentPanelComponent(tree, tui, theme, () => { this.agentPanelClose = undefined; done(undefined); });
-    }, {
-      overlay: true,
-      overlayOptions: { width: "40%", minWidth: 44, maxHeight: "100%", anchor: "top-right", margin: 1, nonCapturing: true, visible: (termWidth) => termWidth >= 100 },
-    });
-  }
-
   /** Live subagent dashboard widget above the editor, refreshed on a light timer. */
   private installAgentWidget(ctx: ExtensionContext): void {
     ctx.ui.setWidget("hm-agents", (tui, theme) => {
@@ -122,5 +108,5 @@ export class SupervisorIntegration {
 
   private shortName(id: string): string { return id.replace(/-[a-f0-9]{8}$/, ""); }
   continueIfNeeded(ctx: ExtensionContext): void { const loop = this.loop; if (!loop || !ctx.isIdle()) return; const state = loop.snapshot(); if (state.status !== "running" || state.iteration <= this.lastScheduledIteration) return; this.lastScheduledIteration = state.iteration; if (ctx.hasUI) ctx.ui.setStatus("hypothesis-machine", `HM ${state.runId} · iteration ${state.iteration + 1}`); this.pi.sendUserMessage(`Continue bounded research run ${state.runId} with iteration ${state.iteration + 1}. Reassess unknowns and contradictions, use agents only where they add information, then call research_control record_iteration. Stop when its coded state is no longer running.`); }
-  async shutdown(): Promise<void> { this.agentPanelClose?.(); this.agentPanelClose = undefined; if (this.widgetTimer) { clearInterval(this.widgetTimer); this.widgetTimer = undefined; } this.requestAgentRender = undefined; await this.tree?.shutdown(); this.memory?.close(); this.tree = undefined; }
+  async shutdown(): Promise<void> { if (this.widgetTimer) { clearInterval(this.widgetTimer); this.widgetTimer = undefined; } this.requestAgentRender = undefined; await this.tree?.shutdown(); this.memory?.close(); this.tree = undefined; }
 }