Add config file.

This file should be copied to config.shell.  This way it's more convnenient for end users to not have to always move/redo the config file when the config.shell.smp is modified.
Added last edit_these.sh variables to this file
Remove edit_these.sh

These functions were moved to config.shell.smp
Modify the set_perms.sh to use the config file.

Tidied some things up, and streamlined the subdir permissions check
Added .gitignore to ignore locally modified config.shell