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Personal AI Infrastructure (PAI) - Root

Context & Intent

This is the root of the METAINFORMANT executable.

Intent: Provide a comprehensive, modular, production-ready bioinformatics toolkit.
State: As of Feb 2026, the repo is in a "Stabilized" state with high modularity and production-ready RNA-seq pipeline.

Virtual Hierarchy

src/: Core business logic.
scripts/: Thin orchestration layer.
docs/: User-facing documentation.
tests/: No-mock verification suite.

Maintenance Notes

Do not use mocks: Always prefer real implementations.
Use uv: Strict dependency management.
Output Isolation: All artifacts go to output/.

AI Workflows

Refactoring: When modifying src/, always run scripts/run_all_scripts.py to verify regressions.
Documentation: Keep AGENTS.md and README.md synchronized with code changes.