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mitochondrial_map.md

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The Mitochondrial Map -> Biological Sovereignty

This document catalogs the existing structural reflexes of the QuanuX cell. These are the "Organelles"—the form-fitting membranes insulating the core cellular receptors. In accordance with Operation "Mitochondrial Synthesis", these files exist in a state of Biological Sovereignty and have not been altered or relocated.

They are presented here for biological classification and mapping toward the new structural man pages.

I. The Core Receptors (The Cell Nucleus)

These files represent the irreducible math—the absolute DNA of the cell.

  • docs/IMMORTAL_RATIONALE.md

    • Organelle Descriptor: The Genetic Chronicle. The absolute historical memory of the cellular lineage.
    • Manual Recommendation: Map to man/man7/quanux-cell.7 (The Preamble).

  • docs/SIM_LIVE_PARITY.md

    • Organelle Descriptor: The Replication Integrity Sequence. Proves the mitosis of the simulated strategy perfectly copies the live strategy.
    • Manual Recommendation: Map to man/man7/quanux-cell.7 and man/man2/ritchie-interlock.2.

  • docs/man/quanux-rubicon.1

    • Organelle Descriptor: The Immunity Array. The structural defense against the "Institutional 8" external pathogens.
    • Manual Recommendation: Embed as a primary defensive reflex in man/man7/quanux-cell.7 (The Russian Doll insulation logic).

II. The Insulation Membranes (The Russian Dolls)

These files act as the organelles insulating the Core 3 Execution Spreader from the Core 5 Sentinel interlock.

  • docs/INSTITUTIONAL_REFERENCE.md

    • Organelle Descriptor: The Receptor Threshold limits. The physical limits before the cell undergoes STATE_HALT apoptosis.
    • Manual Recommendation: Map to man/man2/ritchie-interlock.2 (The Cellular Invariants).

  • docs/man/quanux-fsm-diagram.1

    • Organelle Descriptor: The Cytoskeleton. The absolute pathways and state transitions the organelle may traverse.
    • Manual Recommendation: Map directly into man/man2/ritchie-interlock.2.

  • .agent/skills/execution_stack.yml

    • Organelle Descriptor: The Core Binding Ribosomes. Physically commanding agents on exactly which cellular nodes they are allowed to synthesize.
    • Manual Recommendation: Map to man/man3/quanux-organelles.3 (Extension Growth APIs).

III. The Scribe & Synapse Fragments (The Neural Edge)

These act as the cellular memory output and the network connectivity layers.

  • docs/man/quanux-vault.1 & .agent/skills/reconciliation.yml

    • Organelle Descriptor: The HDF5 Vacuole. Safely storing the binary structural memory of the cell without interfering with its living cycle.
    • Manual Recommendation: Secondary membrane reference in man/man3/quanux-organelles.3.

  • docs/man/quanux-adapter-live.1 & docs/man/quanux-adapter-sim.1

    • Organelle Descriptor: The External Synapses. The redundant connections binding the Sovereign Cell to external market data fluids.
    • Manual Recommendation: Mentioned broadly in man/man7/quanux-cell.7 as the outer cell wall.

The Architect's Recommendation

These existing fragments represent an extremely high-fidelity genome. To transition to the "Russian Doll" semantic mapping, the new structural pages (quanux-cell.7, ritchie-interlock.2, quanux-organelles.3) should synthesize this genetic logic.