docs: ADR link fixes (superseded by #9)#8
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A pass over the codebase before going public. None of these change behavior; they all make the repo read better as a finished artefact rather than an in-progress build. Source comments: - `ingestion/pipeline.py`, `retrieval/embedder.py`, `generation/generator.py`, and `tests/test_config.py` carried docstrings that referenced "Layer 3", "Layer 5", "PR 1", etc. Those were notes for the build process and don't mean anything to a reader landing on the public repo. Reworded to describe what the code does, without the timeline. ADR cross-links: - The seven ADRs used `[[001-name]]` memory-style links that render as literal text on GitHub. Replaced with standard `[ADR 001](001-name.md)` markdown so the link graph actually works in the browser. AGENTS.md: - Companion-project list pointed at local filesystem paths under `/Users/adelsaoud/...`. Swapped for GitHub URLs so the agent doc reads the same whether it is browsed on GitHub or referenced by a tool that cannot resolve those local paths.
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Superseded by #9.