Clarify automaton fixer, recipe, and repository helper docstrings

[coderabbitai]

Expand Rust docstrings to describe fixer safety, dry-run and commit behavior, file operations, template expansion, recipe conversion requirements, and repository path resolution. This is documentation-only and matches the task intent. Validation was not run.

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[coderabbitai]

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[hyperpolymath]

Closing: this docstring PR is stacked on fix/restore-fixer-and-clear-path-scars (#507), which has been closed as superseded by #512 + main's own fixer.rs repair (#514).

The documentation intent is already delivered: the merged #512 resolution keeps the rich rustdoc comments on fixer.rs/hypatia.rs/main.rs (canonicalised roots, exclusion-registry enforcement, atomic publish, escaped-colon syntax, repos_base/resolve_repo_path behaviour) — the same functions this PR set out to document. If any specific docstring here is still wanted, a fresh 3-file PR against current main (or against #512's branch) would apply cleanly.