Removed now obsolete CVS substitutions.

Fixed file permissions.

- Fixed bug that caused additional LaTeX options to be incorrectly added.

- Added new makefile infrastructure for general documents. ...

- Created include files for various "standard" items (paths, rules, etc.).
  These will ultimately be used by all the other make include files in
  order to promote standardisation and consistency.
- Removed obsolete Perl script for handling document includes.