Not create empty skeleton dirs for empty variants
    
    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>