Change the init script to not use a skel dir

This allows us to create empty directories without needing hacks like
.gitkeep or another placeholder.
Remove the skel directory
Merge pull request #25 from nickjj/init

Create the skeleton structure through bash instead of a skel dir
Change the Makefile file mode to 0644
Remove support for skel directory from Makefile
Merge pull request #26 from drybjed/makefile-remove-skel

Updates in Makefile
Change the Makefile mode to 644, again.