hypothesis-machine/graphify-out/GRAPH_REPORT.md

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_Community 1
• _COMMUNITY_Community 2
• _COMMUNITY_Community 3
• _COMMUNITY_Community 4
• _COMMUNITY_Community 5
• _COMMUNITY_Community 6
• _COMMUNITY_Community 8
• _COMMUNITY_Community 9
• _COMMUNITY_Community 10
• _COMMUNITY_Community 11
• _COMMUNITY_Community 12
• _COMMUNITY_Community 13
• _COMMUNITY_Community 14
• _COMMUNITY_Community 15
• _COMMUNITY_Community 16
• _COMMUNITY_Community 17
• _COMMUNITY_Community 18
• _COMMUNITY_Community 19
• _COMMUNITY_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.