docs(claude-md): drop 40 lines derivable from the codebase (#174)

/doctor check 3 trim: Key Files table (ls shows it), Core Pipeline +
Key Data Types (API signatures from source), Configuration yaml block
(authoritative copy lives in examples/.codeindex.yaml — kept the one
-line pointer), and the stale v0.25.0 header (the injected codeindex
section already stamps the real version). Keeps all non-derivable
content: gotchas, commit/docs rules, historical decision notes.