User-defined CLAUDE.md rules are overridden by internal system defaults

CLAUDE.md rules should be the highest priority configuration, but internal system defaults silently take precedence.

Example: My global CLAUDE.md explicitly states "no Claude mentions in commits, PRs, or pushes." Despite this, Claude Code consistently adds Co-Authored-By: Claude ... to every commit because of a built-in system instruction. The user-defined rule is completely ignored until the user notices and complains.

Why this matters: If users invest time in defining clear rules and constraints, they need to be able to trust that these rules are respected. Silently overriding them destroys confidence in the entire CLAUDE.md configuration system. What's the point of having customizable rules if built-in defaults win anyway?

Expected behavior: User-defined rules in CLAUDE.md should always take precedence over internal system defaults. No exceptions.