Htaccess Conflicts

Hi,

I modify html/.htaccess as this is where RewriteBase is supposed to be set. But then I often end up with the error message during validate.php,

[WARN]  Your local git contains modified files, this could prevent automatic updates.
Modified files:
	 html/.htaccess

Perhaps Rewrite Base should be stored somewhere else (i.e. not a file tracked in git)?

Thanks!