Agent System — Directory Map

Phase 1: Documentation-only. No paths moved yet.
Phase 2 (planned): physically reorganize into subdirectories after path audit.

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🧠 CORE — The organism's brain and nervous system

Directory	Role
sovereign/	Primary agent daemon — 8 cognitive organs, evolution loop, all active systems
substrate/	Blackboard bus, registry, nerve signals, inter-agent coordination layer
agent-atlas/	Memory infrastructure — daemons, onboarding, context recall, event ledger
shared/	Cross-cutting utilities shared by multiple components
onboarding.py	Session spawn entrypoint — assembles live context at T=0

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🫀 ORGANS — Cognitive modules imported by Sovereign

Directory	Role
adaptive_cognition/	Adaptive routing — learns which strategies work
blueprint_forge/	Blueprint generation engine
cortex/	Primary memory engine (cortex.engine.Cortex)
cortex_graph/	Graph-structured memory
neural_cortex/	Neural pattern memory
code_cortex/	Code-specific memory layer
working_memory/	Short-term working memory
goal-stack/	Goal priority stack
theory-of-mind/	Agent ToM modeling
metacognition/	Self-monitoring, strategy selection
learning-loop/	Learning from outcomes
cognitive-loop/	Cognitive iteration controller
imagination/	Counterfactual / forward sim
counterfactual-engine/	What-if reasoning
cognitive_biases/	Bias detection and correction
context_weave/	Context assembly
priming/	Priming / attention steering
axon/	Signal routing
soma/	Body / metabolic state
synaptic/	Synaptic weighting
spectra/	Spectrum analysis
trace/	Execution trace
vault/	Secure storage
oracle/	Prediction / forecasting
token-metabolism/	Token budget metabolism
vital-signs/	Health monitoring
coherence-gate/	Output coherence gating
gradient-bridge/	Gradient signal bridge
gravity-mesh/	Gravity Well context retrieval mesh

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⚙️ DAEMONS — Long-running background processes

Directory	Role
reaper/	Process lifecycle management — kills zombies, watches health
consistency-daemon/	Memory consistency enforcement (running as root)
grounding-daemon/	Groundedness enforcement (running as root)
consolidation-daemon/	Memory consolidation
daemon-doctor/	Daemon health checker
grounding-daemon/	Grounding enforcement

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📦 PRODUCTS — Shipped or deployed applications

Directory	Role
DB-Memory/	Product container: Manifesto Engine, CortexDB, code-cortex
Locus/	Primary IDE integration product
NewsForge/	News generation and aggregation
ShortForge/	Short-form content generation
SocialBox/	Social media tooling
Games/	Agent game experiments
Mnemos/	Memory product
OriginLens/	Origin tracing tool
Server.MCP.Tools.API.Cloud/	MCP tooling API server
fleet-dashboard/	Multi-agent fleet monitoring
agent-monitor/	Agent monitoring dashboard

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🔧 TOOLS — Dev tooling and utilities

Directory	Role
drift/	Semantic drift detection
sentinel/	Security and guardrails
system-debugger/	System debugging utilities
autopsy/	Post-mortem analysis
agent-spec-manager/	Agent spec management
project-tracker/	Project tracking
repolens/	Repository analysis
route_bench/	Routing benchmarks
agent-prompt-bridge/	Prompt injection bridge (Kiro / IDE integration)
agent-mouse/	Mouse control for desktop agents
desktop-vision-agent/	Desktop vision / screen reading
ionichalo/	IonicHalo pipe — IDE ↔ Sovereign bridge

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🤝 COLLAB & COORDINATION

Directory	Role
agent-collab/	Agent-to-agent collab channel
agent-memory-kit/	Packaged memory SDK for external agents
agentready-ide/	IDE readiness tooling
gradient-bridge/	Gradient signal bridge
knowledge-graph/	Knowledge graph layer
agent_bootstrap/	Agent bootstrapping utilities

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🔬 RESEARCH — Experiments, prototypes, active exploration

Directory	Role
autobio/	Autobiographical memory research
transplant/	Module transplant experiments
synaptic/	Synaptic weighting experiments
forge-projects/	Forge project experiments
workspace/	Scratch workspace
output/	Generation output storage
data/	Raw data storage

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🗺️ Phase 2 — Planned target structure

Agent_System/
├── core/          ← sovereign, substrate, agent-atlas, shared
├── organs/        ← all cognitive modules imported by sovereign
├── daemons/       ← reaper, consistency-daemon, grounding-daemon, consolidation-daemon
├── products/      ← DB-Memory, Locus, NewsForge, ShortForge, etc.
├── tools/         ← drift, sentinel, autopsy, agent-spec-manager, etc.
├── collab/        ← agent-collab, agent-memory-kit, ionichalo
└── research/      ← autobio, transplant, workspace, forge-projects

Phase 2 prerequisites:

1. Audit all sys.path hardcodes across sovereign, substrate, agent-atlas daemons
2. Update .service files to new paths
3. Run full integration test after move
4. Restart all daemons

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Last updated: 2026-03-21 by Antigravity