diagnostics: fix errant warning on httpd conf

Bug 1100169 - oo-diagnostics tools throw warning message when user add
alias cert to app
https://bugzilla.redhat.com/show_bug.cgi?id=1100169

also:
Bug 1002559 - oo-diagnostics should check the mode on important files
https://bugzilla.redhat.com/show_bug.cgi?id=1002559

test_apache_can_read_conf_files is intended to warn when the apache user
cannot read files it needs to. The files being checked are overly broad;
since httpd reads all of its configuration as root before switching to
apache user, none of that needs to be apache-readable. Instead, just
check files that apache will actually be reading at runtime. Everything
related to Rails apps falls into this category.