Update setup.sh to create config dir

Also fix a small typo in setup.sh to fix an error.

Store executable permissions on scripts in git.
Update docs with new installation procedure.

Updates a lot of piotrs documentation to mesh with the changes made, regarding
configuration, and the setup.sh script.
Fix typo on setup script when creating config dir.
Update deployment documentation.

Deployment docs now reflect latest installation procedures.

General cleanup as well.