diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1ae0652..0172181 100644
--- a/CHANGELOG.md
+++ b/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
 
diff --git a/graphify-out/.graphify_labels.json b/graphify-out/.graphify_labels.json
new file mode 100644
index 0000000..3c0e6c1
--- /dev/null
+++ b/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"
+}
diff --git a/graphify-out/.graphify_root b/graphify-out/.graphify_root
new file mode 100644
index 0000000..945c9b4
--- /dev/null
+++ b/graphify-out/.graphify_root
@@ -0,0 +1 @@
+.
\ No newline at end of file
diff --git a/graphify-out/GRAPH_REPORT.md b/graphify-out/GRAPH_REPORT.md
new file mode 100644
index 0000000..df85ca7
--- /dev/null
+++ b/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._
\ No newline at end of file
diff --git a/graphify-out/cache/ast/v0.8.44/1df6daad97435ab70a984f401eab97094277dd7835d479d2967e1ec1623d79fd.json b/graphify-out/cache/ast/v0.8.44/1df6daad97435ab70a984f401eab97094277dd7835d479d2967e1ec1623d79fd.json
new file mode 100644
index 0000000..2a85974
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+++ b/graphify-out/cache/ast/v0.8.44/1df6daad97435ab70a984f401eab97094277dd7835d479d2967e1ec1623d79fd.json
@@ -0,0 +1 @@
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diff --git a/graphify-out/cache/ast/v0.8.44/25868e1e77377761e5f756724739440927cdecf3d48c2800816407ef81b79222.json b/graphify-out/cache/ast/v0.8.44/25868e1e77377761e5f756724739440927cdecf3d48c2800816407ef81b79222.json
new file mode 100644
index 0000000..54fcd04
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\ No newline at end of file
diff --git a/graphify-out/cache/ast/v0.8.44/32246de16c8fb36b826cb70b489f91ee0b3e5073bcbde729853ca04813fda9e4.json b/graphify-out/cache/ast/v0.8.44/32246de16c8fb36b826cb70b489f91ee0b3e5073bcbde729853ca04813fda9e4.json
new file mode 100644
index 0000000..fc363d9
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diff --git a/graphify-out/cache/ast/v0.8.44/33a91ff7d9ddc51110b59f673dea6bf954c48a6fc880f9a06b713dacb6c2c109.json b/graphify-out/cache/ast/v0.8.44/33a91ff7d9ddc51110b59f673dea6bf954c48a6fc880f9a06b713dacb6c2c109.json
new file mode 100644
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diff --git a/graphify-out/cache/ast/v0.8.44/49863ef1ecd0b134189964c301f95090bf082241233c16055decd9aca6a9a314.json b/graphify-out/cache/ast/v0.8.44/49863ef1ecd0b134189964c301f95090bf082241233c16055decd9aca6a9a314.json
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diff --git a/graphify-out/cache/stat-index.json b/graphify-out/cache/stat-index.json
new file mode 100644
index 0000000..4207857
--- /dev/null
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diff --git a/graphify-out/graph.html b/graphify-out/graph.html
new file mode 100644
index 0000000..f961fba
--- /dev/null
+++ b/graphify-out/graph.html
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+<!DOCTYPE html>
+<html lang="en">
+<head>
+<meta charset="UTF-8">
+<title>graphify - graphify-out/graph.html</title>
+<script src="https://unpkg.com/vis-network@9.1.6/standalone/umd/vis-network.min.js"
+        integrity="sha384-Ux6phic9PEHJ38YtrijhkzyJ8yQlH8i/+buBR8s3mAZOJrP1gwyvAcIYl3GWtpX1"
+        crossorigin="anonymous"></script>
+<style>
+  * { box-sizing: border-box; margin: 0; padding: 0; }
+  body { background: #0f0f1a; color: #e0e0e0; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", sans-serif; display: flex; height: 100vh; overflow: hidden; }
+  #graph { flex: 1; }
+  #sidebar { width: 280px; background: #1a1a2e; border-left: 1px solid #2a2a4e; display: flex; flex-direction: column; overflow: hidden; }
+  #search-wrap { padding: 12px; border-bottom: 1px solid #2a2a4e; }
+  #search { width: 100%; background: #0f0f1a; border: 1px solid #3a3a5e; color: #e0e0e0; padding: 7px 10px; border-radius: 6px; font-size: 13px; outline: none; }
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+  #search-results { max-height: 140px; overflow-y: auto; padding: 4px 12px; border-bottom: 1px solid #2a2a4e; display: none; }
+  .search-item { padding: 4px 6px; cursor: pointer; border-radius: 4px; font-size: 12px; white-space: nowrap; overflow: hidden; text-overflow: ellipsis; }
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+  #info-panel { padding: 14px; border-bottom: 1px solid #2a2a4e; min-height: 140px; }
+  #info-panel h3 { font-size: 13px; color: #aaa; margin-bottom: 8px; text-transform: uppercase; letter-spacing: 0.05em; }
+  #info-content { font-size: 13px; color: #ccc; line-height: 1.6; }
+  #info-content .field { margin-bottom: 5px; }
+  #info-content .field b { color: #e0e0e0; }
+  #info-content .empty { color: #555; font-style: italic; }
+  .neighbor-link { display: block; padding: 2px 6px; margin: 2px 0; border-radius: 3px; cursor: pointer; font-size: 12px; white-space: nowrap; overflow: hidden; text-overflow: ellipsis; border-left: 3px solid #333; }
+  .neighbor-link:hover { background: #2a2a4e; }
+  #neighbors-list { max-height: 160px; overflow-y: auto; margin-top: 4px; }
+  #legend-wrap { flex: 1; overflow-y: auto; padding: 12px; }
+  #legend-wrap h3 { font-size: 13px; color: #aaa; margin-bottom: 10px; text-transform: uppercase; letter-spacing: 0.05em; }
+  .legend-item { display: flex; align-items: center; gap: 8px; padding: 4px 0; cursor: pointer; border-radius: 4px; font-size: 12px; }
+  .legend-item:hover { background: #2a2a4e; padding-left: 4px; }
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+  .legend-dot { width: 12px; height: 12px; border-radius: 50%; flex-shrink: 0; }
+  .legend-label { flex: 1; overflow: hidden; text-overflow: ellipsis; white-space: nowrap; }
+  .legend-count { color: #666; font-size: 11px; }
+  #stats { padding: 10px 14px; border-top: 1px solid #2a2a4e; font-size: 11px; color: #555; }
+  #legend-controls { display: flex; align-items: center; gap: 8px; margin-bottom: 8px; padding: 4px 0; }
+  #legend-controls label { display: flex; align-items: center; gap: 6px; cursor: pointer; font-size: 12px; color: #aaa; user-select: none; }
+  #legend-controls label:hover { color: #e0e0e0; }
+  .legend-cb, #select-all-cb { appearance: none; -webkit-appearance: none; width: 14px; height: 14px; border: 1.5px solid #3a3a5e; border-radius: 3px; background: #0f0f1a; cursor: pointer; position: relative; flex-shrink: 0; }
+  .legend-cb:checked, #select-all-cb:checked { background: #4E79A7; border-color: #4E79A7; }
+  .legend-cb:checked::after, #select-all-cb:checked::after { content: ''; position: absolute; left: 3.5px; top: 1px; width: 4px; height: 7px; border: solid #fff; border-width: 0 2px 2px 0; transform: rotate(45deg); }
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+</style>
+</head>
+<body>
+<div id="graph"></div>
+<div id="sidebar">
+  <div id="search-wrap">
+    <input id="search" type="text" placeholder="Search nodes..." autocomplete="off">
+    <div id="search-results"></div>
+  </div>
+  <div id="info-panel">
+    <h3>Node Info</h3>
+    <div id="info-content"><span class="empty">Click a node to inspect it</span></div>
+  </div>
+  <div id="legend-wrap">
+    <h3>Communities</h3>
+    <div id="legend-controls">
+      <label><input type="checkbox" id="select-all-cb" checked onchange="toggleAllCommunities(!this.checked)">Select All</label>
+    </div>
+    <div id="legend"></div>
+  </div>
+  <div id="stats">331 nodes &middot; 619 edges &middot; 21 communities</div>
+</div>
+<script>
+const RAW_NODES = [{"id": "eslint_config", "label": "eslint.config.js", "color": {"background": "#F28E2B", "border": "#F28E2B", "highlight": {"background": "#ffffff", "border": "#F28E2B"}}, "size": 10.0, "font": {"size": 0, "color": "#ffffff"}, "title": "eslint.config.js", "community": 21, "community_name": "Community 21", "source_file": "eslint.config.js", "file_type": "code", "degree": 0}, {"id": "package", "label": "package.json", "color": {"background": "#76B7B2", "border": "#76B7B2", "highlight": {"background": "#ffffff", "border": "#76B7B2"}}, "size": 18.2, "font": {"size": 12, "color": "#ffffff"}, "title": "package.json", "community": 3, "community_name": "Community 3", "source_file": "package.json", "file_type": "code", "degree": 12}, {"id": "package_name", "label": "name", "color": {"background": "#76B7B2", "border": "#76B7B2", "highlight": {"background": "#ffffff", "border": "#76B7B2"}}, "size": 10.7, "font": {"size": 0, "color": "#ffffff"}, "title": "name", "community": 3, 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"confidence": "EXTRACTED"}, {"from": "security", "to": "docs_security", "label": "references", "title": "references [EXTRACTED]", "dashes": false, "width": 2, "color": {"opacity": 0.7}, "confidence": "EXTRACTED"}, {"from": "security", "to": "security_security_policy", "label": "contains", "title": "contains [EXTRACTED]", "dashes": false, "width": 2, "color": {"opacity": 0.7}, "confidence": "EXTRACTED"}, {"from": "security_security_policy", "to": "security_reporting_a_vulnerability", "label": "contains", "title": "contains [EXTRACTED]", "dashes": false, "width": 2, "color": {"opacity": 0.7}, "confidence": "EXTRACTED"}, {"from": "security_security_policy", "to": "security_supported_versions", "label": "contains", "title": "contains [EXTRACTED]", "dashes": false, "width": 2, "color": {"opacity": 0.7}, "confidence": "EXTRACTED"}, {"from": "docs_architecture", "to": "docs_architecture_architecture", "label": "contains", "title": "contains [EXTRACTED]", "dashes": false, "width": 2, "color": {"opacity": 0.7}, "confidence": "EXTRACTED"}, {"from": "docs_development", "to": "docs_development_development", "label": "contains", "title": "contains [EXTRACTED]", "dashes": false, "width": 2, "color": {"opacity": 0.7}, "confidence": "EXTRACTED"}, {"from": "docs_pi_capabilities", "to": "docs_pi_capabilities_verified_pi_capabilities_0_83_0", "label": "contains", "title": "contains [EXTRACTED]", "dashes": false, "width": 2, "color": {"opacity": 0.7}, "confidence": "EXTRACTED"}, {"from": "docs_pi_capabilities_verified_pi_capabilities_0_83_0", "to": "docs_pi_capabilities_assumptions_corrected_after_verification", "label": "contains", "title": "contains [EXTRACTED]", "dashes": false, "width": 2, "color": {"opacity": 0.7}, "confidence": "EXTRACTED"}, {"from": "docs_pi_capabilities_verified_pi_capabilities_0_83_0", "to": "docs_pi_capabilities_implemented_here", "label": "contains", "title": "contains [EXTRACTED]", "dashes": false, "width": 2, "color": {"opacity": 0.7}, "confidence": "EXTRACTED"}, {"from": "docs_pi_capabilities_verified_pi_capabilities_0_83_0", "to": "docs_pi_capabilities_reused_from_pi", "label": "contains", "title": "contains [EXTRACTED]", "dashes": false, "width": 2, "color": {"opacity": 0.7}, "confidence": "EXTRACTED"}, {"from": "docs_releasing", "to": "docs_releasing_releasing", "label": "contains", "title": "contains [EXTRACTED]", "dashes": false, "width": 2, "color": {"opacity": 0.7}, "confidence": "EXTRACTED"}, {"from": "docs_releasing", "to": "docs_security", "label": "references", "title": "references [EXTRACTED]", "dashes": false, "width": 2, "color": {"opacity": 0.7}, "confidence": "EXTRACTED"}, {"from": "docs_security", "to": "docs_security_security_model", "label": "contains", "title": "contains [EXTRACTED]", "dashes": false, "width": 2, "color": {"opacity": 0.7}, "confidence": "EXTRACTED"}, {"from": "prompts_agent_base", "to": "prompts_agent_base_recursive_research_agent", "label": "contains", "title": "contains [EXTRACTED]", "dashes": false, "width": 2, "color": {"opacity": 0.7}, "confidence": "EXTRACTED"}, {"from": "prompts_retrospective", "to": "prompts_retrospective_team_retrospective", "label": "contains", "title": "contains [EXTRACTED]", "dashes": false, "width": 2, "color": {"opacity": 0.7}, "confidence": "EXTRACTED"}, {"from": "prompts_supervisor", "to": "prompts_supervisor_hypothesis_machine_supervisor", "label": "contains", "title": "contains [EXTRACTED]", "dashes": false, "width": 2, "color": {"opacity": 0.7}, "confidence": "EXTRACTED"}, {"from": "prompts_synthesis", "to": "prompts_synthesis_synthesis", "label": "contains", "title": "contains [EXTRACTED]", "dashes": false, "width": 2, "color": {"opacity": 0.7}, "confidence": "EXTRACTED"}, {"from": "browser_worker_readme", "to": "browser_worker_readme_browser_use_adapter_contract", "label": "contains", "title": "contains [EXTRACTED]", "dashes": false, "width": 2, "color": {"opacity": 0.7}, "confidence": "EXTRACTED"}];
+const LEGEND = [{"cid": 0, "color": "#4E79A7", "label": "Community 0", "count": 76}, {"cid": 1, "color": "#F28E2B", "label": "Community 1", "count": 34}, {"cid": 2, "color": "#E15759", "label": "Community 2", "count": 34}, {"cid": 3, "color": "#76B7B2", "label": "Community 3", "count": 34}, {"cid": 4, "color": "#59A14F", "label": "Community 4", "count": 12}, {"cid": 5, "color": "#EDC948", "label": "Community 5", "count": 6}, {"cid": 6, "color": "#B07AA1", "label": "Community 6", "count": 39}, {"cid": 8, "color": "#9C755F", "label": "Community 8", "count": 12}, {"cid": 9, "color": "#BAB0AC", "label": "Community 9", "count": 15}, {"cid": 10, "color": "#4E79A7", "label": "Community 10", "count": 15}, {"cid": 11, "color": "#F28E2B", "label": "Community 11", "count": 15}, {"cid": 12, "color": "#E15759", "label": "Community 12", "count": 9}, {"cid": 13, "color": "#76B7B2", "label": "Community 13", "count": 8}, {"cid": 14, "color": "#59A14F", "label": "Community 14", "count": 5}, {"cid": 15, "color": "#EDC948", "label": "Community 15", "count": 4}, {"cid": 16, "color": "#B07AA1", "label": "Community 16", "count": 4}, {"cid": 17, "color": "#FF9DA7", "label": "Community 17", "count": 2}, {"cid": 18, "color": "#9C755F", "label": "Community 18", "count": 2}, {"cid": 19, "color": "#BAB0AC", "label": "Community 19", "count": 2}, {"cid": 20, "color": "#4E79A7", "label": "Community 20", "count": 2}, {"cid": 21, "color": "#F28E2B", "label": "Community 21", "count": 1}];
+
+// HTML-escape helper — prevents XSS when injecting graph data into innerHTML
+function esc(s) {
+  return String(s).replace(/&/g,'&amp;').replace(/</g,'&lt;').replace(/>/g,'&gt;').replace(/"/g,'&quot;').replace(/'/g,'&#39;');
+}
+
+// Build vis datasets
+const nodesDS = new vis.DataSet(RAW_NODES.map(n => ({
+  id: n.id, label: n.label, color: n.color, size: n.size,
+  font: n.font, title: n.title,
+  _community: n.community, _community_name: n.community_name,
+  _source_file: n.source_file, _file_type: n.file_type, _degree: n.degree,
+})));
+
+const edgesDS = new vis.DataSet(RAW_EDGES.map((e, i) => ({
+  id: i, from: e.from, to: e.to,
+  label: '',
+  title: e.title,
+  dashes: e.dashes,
+  width: e.width,
+  color: e.color,
+  arrows: { to: { enabled: true, scaleFactor: 0.5 } },
+})));
+
+const container = document.getElementById('graph');
+const network = new vis.Network(container, { nodes: nodesDS, edges: edgesDS }, {
+  physics: {
+    enabled: true,
+    solver: 'forceAtlas2Based',
+    forceAtlas2Based: {
+      gravitationalConstant: -60,
+      centralGravity: 0.005,
+      springLength: 120,
+      springConstant: 0.08,
+      damping: 0.4,
+      avoidOverlap: 0.8,
+    },
+    stabilization: { iterations: 200, fit: true },
+  },
+  interaction: {
+    hover: true,
+    tooltipDelay: 100,
+    hideEdgesOnDrag: true,
+    navigationButtons: false,
+    keyboard: false,
+  },
+  nodes: { shape: 'dot', borderWidth: 1.5 },
+  edges: { smooth: { type: 'continuous', roundness: 0.2 }, selectionWidth: 3 },
+});
+
+network.once('stabilizationIterationsDone', () => {
+  network.setOptions({ physics: { enabled: false } });
+});
+
+function showInfo(nodeId) {
+  const n = nodesDS.get(nodeId);
+  if (!n) return;
+  const neighborIds = network.getConnectedNodes(nodeId);
+  const neighborItems = neighborIds.map(nid => {
+    const nb = nodesDS.get(nid);
+    const color = nb ? nb.color.background : '#555';
+    return `<span class="neighbor-link" style="border-left-color:${esc(color)}" onclick="focusNode(${JSON.stringify(nid)})">${esc(nb ? nb.label : nid)}</span>`;
+  }).join('');
+  document.getElementById('info-content').innerHTML = `
+    <div class="field"><b>${esc(n.label)}</b></div>
+    <div class="field">Type: ${esc(n._file_type || 'unknown')}</div>
+    <div class="field">Community: ${esc(n._community_name)}</div>
+    <div class="field">Source: ${esc(n._source_file || '-')}</div>
+    <div class="field">Degree: ${n._degree}</div>
+    ${neighborIds.length ? `<div class="field" style="margin-top:8px;color:#aaa;font-size:11px">Neighbors (${neighborIds.length})</div><div id="neighbors-list">${neighborItems}</div>` : ''}
+  `;
+}
+
+function focusNode(nodeId) {
+  network.focus(nodeId, { scale: 1.4, animation: true });
+  network.selectNodes([nodeId]);
+  showInfo(nodeId);
+}
+
+// Track hovered node — hover detection is more reliable than click params
+let hoveredNodeId = null;
+network.on('hoverNode', params => {
+  hoveredNodeId = params.node;
+  container.style.cursor = 'pointer';
+});
+network.on('blurNode', () => {
+  hoveredNodeId = null;
+  container.style.cursor = 'default';
+});
+container.addEventListener('click', () => {
+  if (hoveredNodeId !== null) {
+    showInfo(hoveredNodeId);
+    network.selectNodes([hoveredNodeId]);
+  }
+});
+network.on('click', params => {
+  if (params.nodes.length > 0) {
+    showInfo(params.nodes[0]);
+  } else if (hoveredNodeId === null) {
+    document.getElementById('info-content').innerHTML = '<span class="empty">Click a node to inspect it</span>';
+  }
+});
+
+const searchInput = document.getElementById('search');
+const searchResults = document.getElementById('search-results');
+searchInput.addEventListener('input', () => {
+  const q = searchInput.value.toLowerCase().trim();
+  searchResults.innerHTML = '';
+  if (!q) { searchResults.style.display = 'none'; return; }
+  const matches = RAW_NODES.filter(n => n.label.toLowerCase().includes(q)).slice(0, 20);
+  if (!matches.length) { searchResults.style.display = 'none'; return; }
+  searchResults.style.display = 'block';
+  matches.forEach(n => {
+    const el = document.createElement('div');
+    el.className = 'search-item';
+    el.textContent = n.label;
+    el.style.borderLeft = `3px solid ${n.color.background}`;
+    el.style.paddingLeft = '8px';
+    el.onclick = () => {
+      network.focus(n.id, { scale: 1.5, animation: true });
+      network.selectNodes([n.id]);
+      showInfo(n.id);
+      searchResults.style.display = 'none';
+      searchInput.value = '';
+    };
+    searchResults.appendChild(el);
+  });
+});
+document.addEventListener('click', e => {
+  if (!searchResults.contains(e.target) && e.target !== searchInput)
+    searchResults.style.display = 'none';
+});
+
+const hiddenCommunities = new Set();
+
+const selectAllCb = document.getElementById('select-all-cb');
+
+function updateSelectAllState() {
+  const total = LEGEND.length;
+  const hidden = hiddenCommunities.size;
+  selectAllCb.checked = hidden === 0;
+  selectAllCb.indeterminate = hidden > 0 && hidden < total;
+}
+
+function toggleAllCommunities(hide) {
+  document.querySelectorAll('.legend-item').forEach(item => {
+    hide ? item.classList.add('dimmed') : item.classList.remove('dimmed');
+  });
+  document.querySelectorAll('.legend-cb').forEach(cb => {
+    cb.checked = !hide;
+  });
+  LEGEND.forEach(c => {
+    if (hide) hiddenCommunities.add(c.cid); else hiddenCommunities.delete(c.cid);
+  });
+  const updates = RAW_NODES.map(n => ({ id: n.id, hidden: hide }));
+  nodesDS.update(updates);
+  updateSelectAllState();
+}
+
+const legendEl = document.getElementById('legend');
+LEGEND.forEach(c => {
+  const item = document.createElement('div');
+  item.className = 'legend-item';
+  const cb = document.createElement('input');
+  cb.type = 'checkbox';
+  cb.className = 'legend-cb';
+  cb.checked = true;
+  cb.addEventListener('change', (e) => {
+    e.stopPropagation();
+    if (cb.checked) {
+      hiddenCommunities.delete(c.cid);
+      item.classList.remove('dimmed');
+    } else {
+      hiddenCommunities.add(c.cid);
+      item.classList.add('dimmed');
+    }
+    const updates = RAW_NODES
+      .filter(n => n.community === c.cid)
+      .map(n => ({ id: n.id, hidden: !cb.checked }));
+    nodesDS.update(updates);
+    updateSelectAllState();
+  });
+  item.innerHTML = `<div class="legend-dot" style="background:${c.color}"></div>
+    <span class="legend-label">${c.label}</span>
+    <span class="legend-count">${c.count}</span>`;
+  item.prepend(cb);
+  item.onclick = (e) => {
+    if (e.target === cb) return;
+    cb.checked = !cb.checked;
+    cb.dispatchEvent(new Event('change'));
+  };
+  legendEl.appendChild(item);
+});
+</script>
+<script>
+// Render hyperedges as shaded regions
+const hyperedges = [];
+// afterDrawing passes ctx already transformed to network coordinate space.
+// Draw node positions raw — no manual pan/zoom/DPR math needed.
+network.on('afterDrawing', function(ctx) {
+    hyperedges.forEach(h => {
+        const positions = h.nodes
+            .map(nid => network.getPositions([nid])[nid])
+            .filter(p => p !== undefined);
+        if (positions.length < 2) return;
+        ctx.save();
+        ctx.globalAlpha = 0.12;
+        ctx.fillStyle = '#6366f1';
+        ctx.strokeStyle = '#6366f1';
+        ctx.lineWidth = 2;
+        ctx.beginPath();
+        // Centroid and expanded hull in network coordinates
+        const cx = positions.reduce((s, p) => s + p.x, 0) / positions.length;
+        const cy = positions.reduce((s, p) => s + p.y, 0) / positions.length;
+        const expanded = positions.map(p => ({
+            x: cx + (p.x - cx) * 1.15,
+            y: cy + (p.y - cy) * 1.15
+        }));
+        ctx.moveTo(expanded[0].x, expanded[0].y);
+        expanded.slice(1).forEach(p => ctx.lineTo(p.x, p.y));
+        ctx.closePath();
+        ctx.fill();
+        ctx.globalAlpha = 0.4;
+        ctx.stroke();
+        // Label
+        ctx.globalAlpha = 0.8;
+        ctx.fillStyle = '#4f46e5';
+        ctx.font = 'bold 11px sans-serif';
+        ctx.textAlign = 'center';
+        ctx.fillText(h.label, cx, cy - 5);
+        ctx.restore();
+    });
+});
+</script>
+</body>
+</html>
\ No newline at end of file
diff --git a/graphify-out/graph.json b/graphify-out/graph.json
new file mode 100644
index 0000000..d66bd0c
--- /dev/null
+++ b/graphify-out/graph.json
@@ -0,0 +1,9831 @@
+{
+  "directed": false,
+  "multigraph": false,
+  "graph": {},
+  "nodes": [
+    {
+      "label": "eslint.config.js",
+      "file_type": "code",
+      "source_file": "eslint.config.js",
+      "source_location": "L1",
+      "_origin": "ast",
+      "id": "eslint_config",
+      "community": 21,
+      "norm_label": "eslint.config.js"
+    },
+    {
+      "label": "package.json",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L1",
+      "_origin": "ast",
+      "id": "package",
+      "community": 3,
+      "norm_label": "package.json"
+    },
+    {
+      "label": "name",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L2",
+      "_origin": "ast",
+      "id": "package_name",
+      "community": 3,
+      "norm_label": "name"
+    },
+    {
+      "label": "version",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L3",
+      "_origin": "ast",
+      "id": "package_version",
+      "community": 3,
+      "norm_label": "version"
+    },
+    {
+      "label": "description",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L4",
+      "_origin": "ast",
+      "id": "package_description",
+      "community": 3,
+      "norm_label": "description"
+    },
+    {
+      "label": "keywords",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L5",
+      "_origin": "ast",
+      "id": "package_keywords",
+      "community": 3,
+      "norm_label": "keywords"
+    },
+    {
+      "label": "type",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L11",
+      "_origin": "ast",
+      "id": "package_type",
+      "community": 3,
+      "norm_label": "type"
+    },
+    {
+      "label": "license",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L12",
+      "_origin": "ast",
+      "id": "package_license",
+      "community": 3,
+      "norm_label": "license"
+    },
+    {
+      "label": "files",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L13",
+      "_origin": "ast",
+      "id": "package_files",
+      "community": 3,
+      "norm_label": "files"
+    },
+    {
+      "label": "pi",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L14",
+      "_origin": "ast",
+      "id": "package_pi",
+      "community": 3,
+      "norm_label": "pi"
+    },
+    {
+      "label": "extensions",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L14",
+      "_origin": "ast",
+      "id": "package_pi_extensions",
+      "community": 3,
+      "norm_label": "extensions"
+    },
+    {
+      "label": "scripts",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L15",
+      "_origin": "ast",
+      "id": "package_scripts",
+      "community": 3,
+      "norm_label": "scripts"
+    },
+    {
+      "label": "build",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L16",
+      "_origin": "ast",
+      "id": "package_scripts_build",
+      "community": 3,
+      "norm_label": "build"
+    },
+    {
+      "label": "typecheck",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L17",
+      "_origin": "ast",
+      "id": "package_scripts_typecheck",
+      "community": 3,
+      "norm_label": "typecheck"
+    },
+    {
+      "label": "test",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L18",
+      "_origin": "ast",
+      "id": "package_scripts_test",
+      "community": 3,
+      "norm_label": "test"
+    },
+    {
+      "label": "test:watch",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L19",
+      "_origin": "ast",
+      "id": "package_scripts_test_watch",
+      "community": 3,
+      "norm_label": "test:watch"
+    },
+    {
+      "label": "smoke",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L20",
+      "_origin": "ast",
+      "id": "package_scripts_smoke",
+      "community": 3,
+      "norm_label": "smoke"
+    },
+    {
+      "label": "smoke:installed",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L21",
+      "_origin": "ast",
+      "id": "package_scripts_smoke_installed",
+      "community": 3,
+      "norm_label": "smoke:installed"
+    },
+    {
+      "label": "lint",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L22",
+      "_origin": "ast",
+      "id": "package_scripts_lint",
+      "community": 3,
+      "norm_label": "lint"
+    },
+    {
+      "label": "check",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L23",
+      "_origin": "ast",
+      "id": "package_scripts_check",
+      "community": 3,
+      "norm_label": "check"
+    },
+    {
+      "label": "dependencies",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L25",
+      "_origin": "ast",
+      "id": "package_dependencies",
+      "community": 3,
+      "norm_label": "dependencies"
+    },
+    {
+      "label": "@earendil-works/pi-agent-core",
+      "file_type": "code",
+      "source_file": "package.json",
+      "source_location": "L26",
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\ No newline at end of file
diff --git a/graphify-out/manifest.json b/graphify-out/manifest.json
new file mode 100644
index 0000000..7544d83
--- /dev/null
+++ b/graphify-out/manifest.json
@@ -0,0 +1,272 @@
+{
+  "eslint.config.js": {
+    "mtime": 1785523498.9615993,
+    "ast_hash": "c7b81de2b61a96038029263253de6367",
+    "semantic_hash": ""
+  },
+  "package.json": {
+    "mtime": 1785526465.2095354,
+    "ast_hash": "2175d7849ad80beeb50a48fa8e8fe318",
+    "semantic_hash": ""
+  },
+  "src/agent-factory.ts": {
+    "mtime": 1785524670.1400938,
+    "ast_hash": "858e097f20b3c5dab9fe95a9487bae46",
+    "semantic_hash": ""
+  },
+  "src/agent-spec.ts": {
+    "mtime": 1785524686.056277,
+    "ast_hash": "c2ed4093a8b133a2901f3299f815dffd",
+    "semantic_hash": ""
+  },
+  "src/agent-tree-ui.ts": {
+    "mtime": 1785531669.2444735,
+    "ast_hash": "46092f42e39c542b5322ba4801ae1610",
+    "semantic_hash": ""
+  },
+  "src/agent-tree.ts": {
+    "mtime": 1785529482.8530595,
+    "ast_hash": "23c628c8f9408da01a358077811f9303",
+    "semantic_hash": ""
+  },
+  "src/config.ts": {
+    "mtime": 1785529455.9927368,
+    "ast_hash": "09356c0841160e09eda09a1a121c079a",
+    "semantic_hash": ""
+  },
+  "src/index.ts": {
+    "mtime": 1785530491.219887,
+    "ast_hash": "1846411ba1b6d03e16a11f5aaf768c6c",
+    "semantic_hash": ""
+  },
+  "src/pi-runtime.ts": {
+    "mtime": 1785529526.7125866,
+    "ast_hash": "dca78aafefc1c1d5721fb964aa39d1fb",
+    "semantic_hash": ""
+  },
+  "src/research-loop.ts": {
+    "mtime": 1785527477.5546405,
+    "ast_hash": "6d9e857205ff9a7aab3f6e386fceae2c",
+    "semantic_hash": ""
+  },
+  "src/research-memory.ts": {
+    "mtime": 1785527426.9387124,
+    "ast_hash": "323a51ca7362d3169141bf33fc1a3916",
+    "semantic_hash": ""
+  },
+  "src/run-store.ts": {
+    "mtime": 1785523571.639435,
+    "ast_hash": "2ef9c439c53b389a429f2b7325da8770",
+    "semantic_hash": ""
+  },
+  "src/supervisor.ts": {
+    "mtime": 1785531669.2444735,
+    "ast_hash": "6985f08ed3c8641da3c66e36106e77a1",
+    "semantic_hash": ""
+  },
+  "src/tools/experiment.ts": {
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+    "ast_hash": "d5544b772fac8c3a282857c8f8dc5814",
+    "semantic_hash": ""
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+    "ast_hash": "8e4fe9e60b37d7d7038bafd25fd47039",
+    "semantic_hash": ""
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+  "src/tools/web.ts": {
+    "mtime": 1785528095.958494,
+    "ast_hash": "9dfcfe616c79f4447f993d03ef1a7988",
+    "semantic_hash": ""
+  },
+  "src/types.ts": {
+    "mtime": 1785529455.9937367,
+    "ast_hash": "892d91ef98379ef8f733657cb032eadd",
+    "semantic_hash": ""
+  },
+  "tests/agent-spec.test.ts": {
+    "mtime": 1785524051.1689599,
+    "ast_hash": "4b3a62766fa2bbdf1e3f5abdd1b20f7e",
+    "semantic_hash": ""
+  },
+  "tests/agent-tree.test.ts": {
+    "mtime": 1785529507.101351,
+    "ast_hash": "022be88810f2c08b83c811aec1e47421",
+    "semantic_hash": ""
+  },
+  "tests/confine.test.ts": {
+    "mtime": 1785528537.6857417,
+    "ast_hash": "3058a15651ede931efecbeb0ca724058",
+    "semantic_hash": ""
+  },
+  "tests/experiment.test.ts": {
+    "mtime": 1785528151.0541484,
+    "ast_hash": "fefe14e591263f9817ee924126de59b0",
+    "semantic_hash": ""
+  },
+  "tests/extension-smoke.test.ts": {
+    "mtime": 1785524899.0848217,
+    "ast_hash": "39058644b66fd3e0e77b08c34a6a6d78",
+    "semantic_hash": ""
+  },
+  "tests/helpers.ts": {
+    "mtime": 1785524553.6187508,
+    "ast_hash": "4cb1d4b681689d5d8e0451769b986017",
+    "semantic_hash": ""
+  },
+  "tests/memory.test.ts": {
+    "mtime": 1785527462.459164,
+    "ast_hash": "ffd5cc871a84d750369265c86b7da7d8",
+    "semantic_hash": ""
+  },
+  "tests/pi-agent-runtime.integration.test.ts": {
+    "mtime": 1785524511.7732685,
+    "ast_hash": "db245b752d56fc3df2355ec6536875c7",
+    "semantic_hash": ""
+  },
+  "tests/pi-rpc-smoke.mjs": {
+    "mtime": 1785525841.187079,
+    "ast_hash": "306c7daf2ba5be3110bbbd42c47cc73e",
+    "semantic_hash": ""
+  },
+  "tests/research-loop.test.ts": {
+    "mtime": 1785527442.5569394,
+    "ast_hash": "99d84fb8ec594697e4c998f14f5cc717",
+    "semantic_hash": ""
+  },
+  "tests/web-security.test.ts": {
+    "mtime": 1785524051.1699598,
+    "ast_hash": "760ce533f33a782fa2d803ddb753d60f",
+    "semantic_hash": ""
+  },
+  "tsconfig.build.json": {
+    "mtime": 1785523498.9615993,
+    "ast_hash": "33ea7a02db9bb2bb05e7af22fcac9192",
+    "semantic_hash": ""
+  },
+  "tsconfig.json": {
+    "mtime": 1785523498.9615993,
+    "ast_hash": "bff06dd08c20cf6987e5be1a174fae07",
+    "semantic_hash": ""
+  },
+  ".github/ISSUE_TEMPLATE/bug_report.yml": {
+    "mtime": 1785526202.9694018,
+    "ast_hash": "3d38949573d8e9afbfab15d7aec80208",
+    "semantic_hash": ""
+  },
+  ".github/ISSUE_TEMPLATE/config.yml": {
+    "mtime": 1785526202.9694018,
+    "ast_hash": "74c7aebcc7755d1241890df4fd87c662",
+    "semantic_hash": ""
+  },
+  ".github/ISSUE_TEMPLATE/feature_request.yml": {
+    "mtime": 1785526202.9694018,
+    "ast_hash": "34406f2d63d0509d67ab199c17f3cf9d",
+    "semantic_hash": ""
+  },
+  ".github/dependabot.yml": {
+    "mtime": 1785526202.968402,
+    "ast_hash": "9ae2a4d0a6a13b0e77e3f1608ecc515a",
+    "semantic_hash": ""
+  },
+  ".github/pull_request_template.md": {
+    "mtime": 1785526202.9694018,
+    "ast_hash": "838d15d4640fefb60f534e611607b080",
+    "semantic_hash": ""
+  },
+  ".github/workflows/ci.yml": {
+    "mtime": 1785526202.968402,
+    "ast_hash": "3f93d66df2cec7c5b6d9f523b7a9b8bb",
+    "semantic_hash": ""
+  },
+  ".github/workflows/codeql.yml": {
+    "mtime": 1785526202.968402,
+    "ast_hash": "4e919838522fc9dc44909e4c2d09aa0d",
+    "semantic_hash": ""
+  },
+  ".hypothesis-machine.example.yaml": {
+    "mtime": 1785529501.9182887,
+    "ast_hash": "630dc679669c48ff3578e2d9ed03ad2d",
+    "semantic_hash": ""
+  },
+  "CHANGELOG.md": {
+    "mtime": 1785531669.2434735,
+    "ast_hash": "3d4a048fe013eeba0548c01f00a8504a",
+    "semantic_hash": ""
+  },
+  "CONTRIBUTING.md": {
+    "mtime": 1785526465.2105353,
+    "ast_hash": "ba26a233b0388cf3bc15d68ca1423392",
+    "semantic_hash": ""
+  },
+  "README.md": {
+    "mtime": 1785526465.2095354,
+    "ast_hash": "4f95cd827dc617ee12a1e0f5edfc5f33",
+    "semantic_hash": ""
+  },
+  "SECURITY.md": {
+    "mtime": 1785526202.9664018,
+    "ast_hash": "0a275d04059cdb2913d147ba5a8c11eb",
+    "semantic_hash": ""
+  },
+  "docs/architecture.md": {
+    "mtime": 1785524693.984371,
+    "ast_hash": "4978fcd79045c6ad10f61fbd2de070cb",
+    "semantic_hash": ""
+  },
+  "docs/development.md": {
+    "mtime": 1785526465.2115355,
+    "ast_hash": "aa39cad6227fc294c0b8d4444ef98f09",
+    "semantic_hash": ""
+  },
+  "docs/pi-capabilities.md": {
+    "mtime": 1785525665.6689816,
+    "ast_hash": "3c3098e82aa840cdc4e50eebbc342f5d",
+    "semantic_hash": ""
+  },
+  "docs/releasing.md": {
+    "mtime": 1785526465.2135355,
+    "ast_hash": "8b59c0d5138f4e24b28b1be187c8cd0f",
+    "semantic_hash": ""
+  },
+  "docs/security.md": {
+    "mtime": 1785526465.2135355,
+    "ast_hash": "d1a39881546c3c2a6c80008cf59c3483",
+    "semantic_hash": ""
+  },
+  "infra/compose.yaml": {
+    "mtime": 1785525739.1668599,
+    "ast_hash": "d5264ae5950629e067955aa66cbba7f4",
+    "semantic_hash": ""
+  },
+  "infra/searxng/settings.yml": {
+    "mtime": 1785524192.9155934,
+    "ast_hash": "4d89744864f680a763838d70ff9c8a7c",
+    "semantic_hash": ""
+  },
+  "prompts/agent-base.md": {
+    "mtime": 1785524192.9165936,
+    "ast_hash": "ebc60ed24957c9de9f4dd6087f0e49b1",
+    "semantic_hash": ""
+  },
+  "prompts/retrospective.md": {
+    "mtime": 1785524192.9175935,
+    "ast_hash": "e3f0e1d34e6039038cf6f4f06b08a3e4",
+    "semantic_hash": ""
+  },
+  "prompts/supervisor.md": {
+    "mtime": 1785524192.9165936,
+    "ast_hash": "95a5ee67953ae0f91dc643add2a32db0",
+    "semantic_hash": ""
+  },
+  "prompts/synthesis.md": {
+    "mtime": 1785524192.9165936,
+    "ast_hash": "ce979b164004bdd4d94dcbefd7b00f52",
+    "semantic_hash": ""
+  },
+  "services/browser-worker/README.md": {
+    "mtime": 1785524192.9155934,
+    "ast_hash": "8fa8ac55e56b270cd41ee3608c92928e",
+    "semantic_hash": ""
+  }
+}
\ No newline at end of file
diff --git a/src/agent-tree-ui.ts b/src/agent-tree-ui.ts
index 133b70b..30c5f82 100644
--- a/src/agent-tree-ui.ts
+++ b/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,
diff --git a/src/index.ts b/src/index.ts
index 2769829..f504ee2 100644
--- a/src/index.ts
+++ b/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"); } });
diff --git a/src/supervisor.ts b/src/supervisor.ts
index 2064ef7..7c8dc49 100644
--- a/src/supervisor.ts
+++ b/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; }
 }