- use standard *.sh, *.csh endings

editing the respective settings files.

- foamEtcFile is used to find the files, thus follows the standard
  ~OpenFOAM/fileName expansion mechanism.

- make it easier for non-emacs users to generate some of the
  documentation

- only ignore html files in the main directory, not everywhere.
  This is how we lost FoamFooter.html, FoamHeader.html in doc/Doxygen/ in
  the 1.6.x release

- partial revert for
  commit 9557f2cb

- Rename to a corresponding backup file
  If the backup file already exists, attempt with "01" .. "99" suffix.

- git ignore indexed backup files too

- handle ThirdParty-VERSION properly

- handle wmake/utilbin/ location

- should the wmake/rules/* really be packed with a binary distribution?
  I think this is just left over from before.

- in .gitignore, added other common build targets to be ignored.
  Finalized the move of wmkdep etc to wmake/utilbin/

- the $WM_PROJECT_DIR/.build file is automatically updated.
  This file is (and must be) ignored by git.