[docxology]

Adds README.md and AGENTS.md to every directory in the repository that a contributor or agent enters.

Coverage

• New AGENTS.md (15): repository root, .github, .github/workflows, .aii, src, src/biofirm, src/biofirm/data, tests, tools, models, Documentation, Documentation/Notebooks, Bio_Perplexity, One_Earth, Stream.
• New README.md (13): all of the above except the repository root and models/, whose existing README files were already current and are unchanged.
• Documentation/ and src/ contain no files besides their own guides and their subdirectories; that is stated in their guides. No directory was skipped.

Content

Each guide records:

• what the directory contains and why;
• the check commands that must pass;
• generated versus hand-written files (artifacts and caches are excluded; the hashed requirements export is derived at run time and never committed);
• custody-critical paths (GNN specification and matrices, pin record, version source, packaged configuration, .gitleaksignore);
• traps (lockfile update on pin changes, 90% coverage floor, strict mypy scope, no shell or magic commands in notebooks, offline by default, historical material stays labelled).

Verification

• uv run python tools/verify_repository.py passes. It checks every relative markdown link, the nine required documents, source-data structure, notebook policy, and credential patterns.
• No Python changed, so no test behavior is affected.