repo_config: do not let globals override repo settings

This makes it possible to activate the enable_commit_graph,
enable_log_filecount, and enable_log_linecount for individual
repositories, even if the global setting is "0" (default).

The commit that introduced the broken behavior was e189344, and the
commit message of that makes it clear that this wasn't the intended
behavior.

Signed-off-by: Jason A. Donenfeld <Jason@zx2c4.com>