refactor: extract subdirs list into array
refactor: transform constant to variable
refactor: remove special case for parent dir by moving into loop
avoid custom umask

It's probably better to have directory creation stanardized in
Genome::Sys->create_directory than to have custom permissions in a tool.
Just by coindience Genome::Sys->create_directory uses the same umask.
transform constant to configured variable, GENOME_SYS_UMASK
Merge branch 'AR-271' to move disk permissions to config