CLAUDE.md commit conventions overridden by system prompt defaults

Description

Project-level CLAUDE.md commit conventions are being ignored in favor of the built-in system prompt commit template, even after CLAUDE.md has been explicitly read in the same session.

CLAUDE.md rules that were violated

1. "DO NOT list Claude as author or co-author" — Claude added a Co-Authored-By line anyway, following the system prompt's default commit template
2. "One module per commit" — Claude combined changes to AC_Fence and AP_Scripting into a single commit instead of splitting per subsystem

The CLAUDE.md header states: "These instructions OVERRIDE any default behavior and you MUST follow them exactly as written."

Steps to reproduce

1. Create a CLAUDE.md with commit rules that conflict with the system prompt defaults (e.g., no co-author lines, one module per commit)
2. Ask Claude to read CLAUDE.md at the start of the session
3. Make changes across multiple modules and ask Claude to commit
4. Observe that Claude falls back on the system prompt commit template instead of applying the CLAUDE.md overrides

Expected behavior

CLAUDE.md commit conventions should take precedence over the system prompt's default commit template when they conflict.

Actual behavior

Claude acknowledged the CLAUDE.md rules but used the default commit template anyway, adding Co-Authored-By and combining multiple modules into one commit.