- A few without a 'cd' at the start.
  Use $(getApplication) directly in more places (for clarity).

- A few without a 'cd' at the start.
  Several remove files that are already covered by the cleanCase function.

Uses a system/caseProperties file to select templates from
etc/caseDicts/createZeroDirectoryTemplates to enable high-level setup
of a case.
See
- etc/caseDicts/createZeroDirectoryTemplates
- tutorials/preProcessing/createZeroDirectory