LICENSE
MANIFEST.in
Makefile
NOTICE
README.md
VERSION
pyproject.toml
.soma/cells/README.md
.soma/cells/chloroplasts/.gitkeep
.soma/cells/chloroplasts/persona-bash-architect.md
.soma/cells/chloroplasts/persona-cross-platform-qa.md
.soma/cells/chloroplasts/persona-mcp-specialist.md
.soma/cells/membranes/.gitkeep
.soma/cells/membranes/membrane-enzymes.md
.soma/cells/membranes/membrane-genome-mutations.md
.soma/cells/membranes/membrane-install.md
.soma/cells/plasmodesmata/.gitkeep
.soma/cells/plasmodesmata/contract-mcp-cli-parity.md
.soma/cells/plasmodesmata/contract-sdk-feature-parity.md
.soma/cells/vacuoles/.gitkeep
.soma/cells/vacuoles/trap-ascii-art-render.md
.soma/cells/vacuoles/trap-fix-one-not-all.md
.soma/cells/vacuoles/trap-future-annotations.md
.soma/cells/vacuoles/trap-happy-path-only-tests.md
.soma/cells/vacuoles/trap-hardcoded-paths.md
.soma/cells/vacuoles/trap-install-paths.md
.soma/cells/vacuoles/trap-local-green-ci-red.md
.soma/cells/vacuoles/trap-magic-numbers.md
.soma/cells/vacuoles/trap-orphaned-module.md
.soma/cells/vacuoles/trap-pytest-exit-code.md
.soma/cells/vacuoles/trap-schema-test-gap.md
.soma/cells/vacuoles/trap-stale-rename-refs.md
.soma/cells/vacuoles/trap-subagent-output.md
.soma/cells/vacuoles/trap-test-coverage-horizon.md
.soma/cells/vacuoles/trap-unverified-delegation.md
.soma/cells/vacuoles/trap-version-drift.md
.soma/cells/walls/.gitkeep
.soma/cells/walls/trap-bugfix-without-regression-test.md
.soma/cells/walls/trap-convention-assumption.md
.soma/cells/walls/trap-doc-feature-drift.md
.soma/cells/walls/trap-fail-open-verification.md
.soma/cells/walls/trap-format-code-injection.md
.soma/cells/walls/trap-ghost-cli-flags.md
.soma/cells/walls/trap-layer-violation.md
.soma/cells/walls/trap-path-traversal.md
.soma/cells/walls/trap-recurring-finding-escape.md
.soma/cells/walls/trap-roadmap-status-drift.md
.soma/cells/walls/trap-schema-contract-drift.md
.soma/cells/walls/trap-shell-true-portability.md
.soma/cells/walls/trap-stdout-protocol-corruption.md
.soma/cells/walls/trap-tautological-test.md
.soma/cells/walls/trap-threshold-spec-drift.md
.soma/cells/walls/trap-unregistered-bug-fix.md
.soma/cells/walls/wall-core-installers.md
.soma/cells/walls/wall-deterministic-arbitration.md
.soma/cells/walls/wall-dogfood-own-tools.md
.soma/cells/walls/wall-install-uninstall-parity.md
.soma/cells/walls/wall-mcp-zero-deps.md
.soma/cells/walls/wall-oracles.md
.soma/cells/walls/wall-safety-gate.md
.soma/dreams/2026-09-29.md
.soma/evidence/.fitness.lock
.soma/evidence/.gitignore
.soma/evidence/README.md
.soma/evidence/arbitration_cycle_2.json
.soma/evidence/arbitration_cycle_3.json
.soma/evidence/outcomes.jsonl
enzymes/bayesian_score.py
enzymes/cell_adapt.py
enzymes/cell_adversarial.py
enzymes/cell_coverage.py
enzymes/cell_create_nl.py
enzymes/cell_crossover.py
enzymes/cell_demote.py
enzymes/cell_deps.py
enzymes/cell_enforce.py
enzymes/cell_escaped_defects.py
enzymes/cell_expiry.py
enzymes/cell_fitness.py
enzymes/cell_genesis_stochastic.py
enzymes/cell_metamorphose.py
enzymes/cell_promote.py
enzymes/cell_quorum.py
enzymes/cell_scan.py
enzymes/cell_tournament.py
enzymes/ci_outcome_reporter.py
enzymes/escalation_sentinel.py
enzymes/evidence_collector.py
enzymes/fitness_landscape.py
enzymes/fitness_updater.py
enzymes/hgt_ribosome.py
enzymes/immune_entropy.py
enzymes/immune_grade.py
enzymes/immune_replay.py
enzymes/immune_trends.py
enzymes/inference_provider.py
enzymes/insight_capture.py
enzymes/insight_correlator.py
enzymes/oracle_checkpoint.py
enzymes/outcome_engine.py
enzymes/resilience_engine.py
enzymes/soma_coherence.py
enzymes/soma_interoception.py
enzymes/soma_resolve.py
enzymes/soma_sleep.py
enzymes/sweep_session.py
enzymes/token_census.py
enzymes/ttc_oracle.py
enzymes/ttc_verifier.py
enzymes/verify_bug_registry.py
enzymes/verify_readme_claims.py
genome/META.md
genome/ci-green-before-release.md
genome/core-change-protocol.md
genome/cost-optimization.md
genome/desktop-automation.md
genome/destructive-ops.md
genome/gitflow-review-gate.md
genome/hgt-resource-consolidation-hgt.md
genome/no-pre-existing-excuse.md
genome/providence.md
genome/subagent-delegation.md
genome/.oracles/architectural-tenets.md
genome/.oracles/documentation.md
genome/.oracles/feature-specs.md
genome/.oracles/git-workflow.md
genome/.oracles/optional-import-guard.md
genome/.oracles/polyglot-standards.md
genome/.oracles/tdd-protocol.md
genome/.oracles/testing.md
immune_system/__init__.py
immune_system/verification/__init__.py
immune_system/verification/arbiter.py
immune_system/verification/branch_coverage.py
immune_system/verification/call_graph.py
immune_system/verification/checkpoint_checks.py
immune_system/verification/immune_verify.py
immune_system/verification/import_guard.py
immune_system/verification/lifecycle.py
immune_system/verification/mutation_tester.py
immune_system/verification/persistence_checker.py
immune_system/verification/quality_gate.py
immune_system/verification/review_adapter.py
immune_system/verification/runner.py
immune_system/verification/transcript_verifier.py
install/hooks.json.template
install/install.ps1
install/install.sh
install/soma.conf.example
install/starter_pack.txt
install/uninstall.ps1
install/uninstall.sh
install/hooks/pre-commit
organs/adaptive-reviewer/SKILL.md
organs/domain-researcher/SKILL.md
organs/genesis/SKILL.md
organs/governance-auditor/SKILL.md
organs/incident-debug/SKILL.md
organs/performance-audit/SKILL.md
organs/post-mortem/SKILL.md
organs/readme-writer/SKILL.md
organs/refactoring-pilot/SKILL.md
organs/security-audit/SKILL.md
organs/session-monitor/SKILL.md
organs/session-preflight/SKILL.md
organs/spec-synthesizer/SKILL.md
organs/staff-review/SKILL.md
organs/visual-analyst/SKILL.md
soma_cli/__init__.py
soma_cli/checkpoint.py
soma_cli/cli.py
soma_cli/demote.py
soma_cli/doctor.py
soma_cli/genesis.py
soma_cli/genesis_generator.py
soma_cli/genesis_scanner.py
soma_cli/init.py
soma_cli/oracle.py
soma_cli/promote.py
soma_cli/report.py
soma_cli/status.py
soma_cli/sync.py
soma_cli/verify.py
soma_cli/starter_rules/cost-optimization.md
soma_cli/starter_rules/destructive-ops.md
soma_cli/starter_rules/git-workflow.md
soma_cli/starter_rules/providence.md
soma_cli/starter_rules/testing.md
soma_governance.egg-info/PKG-INFO
soma_governance.egg-info/SOURCES.txt
soma_governance.egg-info/dependency_links.txt
soma_governance.egg-info/entry_points.txt
soma_governance.egg-info/requires.txt
soma_governance.egg-info/top_level.txt
soma_mcp/__init__.py
soma_mcp/__main__.py
soma_mcp/cell_cache.py
soma_mcp/jit_engine.py
soma_mcp/server.py
soma_mcp/tools.py
soma_sdk/__init__.py
soma_sdk/analysis.py
soma_sdk/cells.py
soma_sdk/errors.py
soma_sdk/governance.py
soma_sdk/invariants.py
soma_sdk/py.typed
soma_sdk/scoring.py
soma_sdk/telemetry.py
templates/README.md
templates/data-pipeline/membrane-source-of-truth-change.md
templates/data-pipeline/vacuole-schema-drift.md
templates/data-pipeline/wall-idempotent-processing.md
templates/incident-response/effector-template.md
templates/incident-response/memory-template.md
templates/infrastructure/membrane-production-deploy.md
templates/infrastructure/vacuole-terraform-drift.md
templates/infrastructure/wall-no-hardcoded-secrets.md
templates/rl-training/membrane-reward-escalation.md
templates/rl-training/vacuole-observation-leakage.md
templates/rl-training/vacuole-reward-exploitation.md
templates/rl-training/wall-checkpoint-invariants.md
templates/rl-training/wall-gradient-health.md
templates/web-backend/membrane-database-migration.md
templates/web-backend/vacuole-n-plus-one-queries.md
templates/web-backend/wall-auth-immutability.md
tests/test_bayesian_correctness.py
tests/test_bayesian_fitness.py
tests/test_bug_registry.py
tests/test_cell_cache.py
tests/test_cell_create_insight.py
tests/test_cell_deps_behavioral.py
tests/test_cell_expiry.py
tests/test_ci_outcome_reporter.py
tests/test_cli.py
tests/test_cli_checkpoint.py
tests/test_cli_demote.py
tests/test_cli_oracle.py
tests/test_cli_promote.py
tests/test_cli_sync.py
tests/test_cli_verify.py
tests/test_credit_assignment.py
tests/test_critical_fixes.py
tests/test_crossover_structured.py
tests/test_decay_integration.py
tests/test_doctor.py
tests/test_enforce_hooks.py
tests/test_enforcement_ladder.py
tests/test_error_handling.py
tests/test_escaped_defects.py
tests/test_evidence_collector.py
tests/test_exponential_decay.py
tests/test_fitness_updater.py
tests/test_gate_invariant_dsl.py
tests/test_genesis.py
tests/test_init.py
tests/test_init_hooks.py
tests/test_insight_capture.py
tests/test_insight_correlator.py
tests/test_install_lifecycle.py
tests/test_integration_lifecycle.py
tests/test_jit_engine_behavioral.py
tests/test_keyring_integration.py
tests/test_lifecycle.py
tests/test_local_promotion_decay.py
tests/test_mcp_capture_insight.py
tests/test_mcp_tools_contract.py
tests/test_mcp_verify.py
tests/test_oracle_checkpoint.py
tests/test_outcome_engine.py
tests/test_outcome_engine_insights.py
tests/test_quality_gate.py
tests/test_quorum.py
tests/test_report.py
tests/test_review_adapter.py
tests/test_review_intensity.py
tests/test_rule_content.py
tests/test_rule_metadata.py
tests/test_sdk_behavioral.py
tests/test_static_invariants.py
tests/test_status.py
tests/test_supercell_cells.py
tests/test_sync_bugfix4.py
tests/test_telemetry.py
tests/test_telemetry_bugfixes.py
tests/test_threshold_recalibration.py
tests/test_tournament_integration.py
tests/test_transcript_verifier_insights.py