Update bash-template to bring in line with recent scripts

Some of the more notable changes:

- Replace 'command' with 'cmd' because 'command' is a shell built-in
- Group `commands` and `help` together in a 'Default Commands' section
  in order to make it easier to add new commands to the end and keep
  them separate.
- Splitting desc set and printing to separate functions.
- Ensure naming is consistent by always using either `$cmd` or 'command'
  when referring to program commands.
- Moving main script handling to function grouped with options and
  environment settings.
Renaming 'bash-templtate' to 'bash-with-commands'