The Makefiles are now in the makefiles sub-directory

The "-f | -force" option in wmakeLnInclude is now "-u | -update" for
consistency with the other scripts.

The "Usage" entry in the headers is now consistently formatted in all
scripts.

This reverts commit c5bea524.

This reverts commit 2e1e671d.

- more consistent script names
- remove '-help' option from internal scripts

- solves problems that can occur when checking $PWD and links are involved

  - send error messages to stderr
  - added -h/-help options where some were missing
  - changed 3-space to 4-space indentation
  - where possible, allow multiple directories from the command-line

  - removed legacy foamDiffSourceList, foamPackChanged
  - added foamPackDoxygen for separate distribution of docs
    handles -prefix option
  - misc. cosmetic changes