Organism model

Flock treats the harness as a living organism: genomes express coordination parameters, circulation vitals track field health, and an immune gate rejects harmful topology mutations.

Status: Phases 1–4 complete (circulation, DNA lineage, immune gate, per-zone expression).

Architecture

flock-core/organism.rs     DNA types + circulation vitals + zone expression
flock-substrate/pheromone  per-zone decay (fallback to global lambda)
flock-runtime/circulation  vitals + immune_fever tracking
flock-runtime/engine.rs    vitals + genome_id + fever + decay wire-through
flock-evolve/genome.rs     lineage + crossover + archive reconstruction
flock-evolve/immune.rs     corpus threat detection + auto_reject
flock-evolve/mutator.rs    crossover + cold-zone decay adjustment
flock-cli/organism_cmd.rs  flock vitals | flock genome list|lineage

Organism loop

flowchart LR
    RUN[flock run] --> VITALS[circulation vitals]
    VITALS --> EP[episode JSON]
    EP --> EV[flock evolve]
    EV --> IMM[immune_report]
    IMM -->|accept| ARCH[genome archive]
    IMM -->|reject| QUAR[quarantine]

    class RUN,VITALS,EP runtime
    class EV,ARCH evolve
    class IMM,QUAR gate

FlockGenome expresses coordination + decay params at episode end
PheromoneField circulation → CirculationVitals in episode
flock evolve mutates or crossover (Pareto ≥ 2) → immune_report() gates accept
Quarantined genomes excluded from archive.nearest() seed
Per-zone decay tuned from proposer cold-zone heatmap

CLI

flock run --goal "reach target" --plugin gridworld
flock vitals
flock evolve --episodes 10
flock genome list
flock genome lineage <genome_id>

Phase completion

Phase	Deliverable	Status
1 Circulation	`circulation_vitals`, `flock vitals`, fitness dimension	✅
2 DNA	`genome_id` lineage, archive seed reconstruction, `flock genome`	✅
3 Immune	drift + fitness + immune gate, quarantine, fever deposit	✅
4 Expression	per-zone decay, crossover, flux-grid test, fever unit test	✅

flux-grid (optional)

Feature: flock-substrate/flux-grid (vendored 64×64 Stigmergy grid)
Not enabled in default builds — zone-keyed PheromoneField remains default substrate
Enable for experiments: cargo build -p flock-substrate --features flux-grid

Known deferred

flux-grid in swarm-demo default path
Full parent_ids lineage CLI (crossover sets parent_ids; CLI shows primary parent_genome_id only)
RAH_MAX_DEPTH in flock-core (cycle avoidance with flock-evolve ↔ flock-rah)

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