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.
Merge pull request #5444 from sosiouxme/bz1100169

Merged by openshift-bot
Bug 1100648 - Fixed formatting of man page
Automatic commit of package [rubygem-openshift-origin-node] release [1.25.4-1].
Automatic commit of package [rubygem-openshift-origin-console] release [1.25.3-1].
Automatic commit of package [rubygem-openshift-origin-common] release [1.24.2-1].
Automatic commit of package [openshift-origin-node-util] release [1.24.3-1].
Merge pull request #5446 from jwhonce/bug/1100648

Merged by openshift-bot
Bug 1100619 - Uppercase primary cartridge name for use in env vars
Merge pull request #5447 from jwhonce/bug/1100619

Merged by openshift-bot
Bug 1100743 - Validate manifest endpoint element
Bug 1100743 - Validate manifest endpoint element

* Add test for empty elements as well
Merge pull request #5449 from jwhonce/bug/1100743

Merged by openshift-bot
system arch guide docs - update gear directories
Make READMEs in template repos more obvious

https://trello.com/c/dKJfwLdh - origin_cartridge_170

Also, remove unnecessary .gitkeep files and replace duplicated
'ruby/versions/{1.8,1.9}/template/.openshift/*' files with
directory symlink to 'ruby/versions/shared/template/.openshift/'.
Merge pull request #5451 from VojtechVitek/improve_template_repo_readmes

Merged by openshift-bot
Change GroupOverride.empty? so group overrides with 1 component is not considered empty.
Change logic that splits group overrides up if their component don't belong to the same platform.
Automatic commit of package [rubygem-openshift-origin-node] release [1.25.5-1].
Automatic commit of package [openshift-origin-cartridge-jbosseap] release [2.18.2-1].
Automatic commit of package [openshift-origin-cartridge-jbossews] release [1.24.2-1].