docs: update TODO and AGENTS for v0.4.0 completion
- Mark v0.4.0 as complete in TODO.md with all phases checked - Update Phase 4 items with actual outcomes - Next step: Track A 99Tc spectrum-shape analysis - Add AGENTS instruction to update project metadata on significant structural changes (package additions, version bumps, etc.)
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@@ -25,6 +25,7 @@ Install: `source ~/.pyenv/sci/bin/activate && pip install -e ".[dev]"`
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- **Commit each logical change** — don't wait for green. Use `git add -p`.
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- **Rebase over merge** for linear history: `git rebase main` before merge.
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- Delete branch locally + remotely after merge.
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- **Update project metadata on significant changes:** When a commit changes the package structure, adds/removes modules, or bumps the version, also update `TODO.md` and `README.md` to reflect the new state. This keeps documentation in sync with code.
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## TDD
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