Do not create empty skeleton dirs for empty variants which we do for rpm
variants in some phases (some others already have the check):
1. createiso phase
2. extra_files phase
3. gather phase
In addtion to this, compose metadata (composeinfo.json) doesn't include
variant paths which don't exist or are just empty dirs now.
Fixes: #497
Merges: #572
Signed-off-by: Qixiang Wan <qwan@redhat.com>