- also add some comments about the side-effects

Based on patch contributed by Alexey Matveichev
Resolves feature request http://bugs.openfoam.org/view.php?id=2328

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.

- reduces verbosity for dynamicCode

- non-silent wmakeLnInclude output to stderr to avoid polluting logs

This reverts commit c5bea524.

This reverts commit 2e1e671d.

- not required since the addition of the '-f' option

- this seems to be the most sensible solution.
  The changed time stamps on the links doesn't seem to bother make at all.

 - useful for avoiding links on older versions, or for 'hiding' contents

  - 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

  - fixed typo: had skipped '-Make' instead of 'Make' directory

  - remove broken links first
    * helps when file locations have changed

  - filter out trailing 'lnInclude' from the <dir> spec
    * this makes it easier to update existing lnInclude dirs:
         find -name lnInclude -exec wmakeLnInclude -f {} \;

  - reduced output noise when re-creating an identical link

specifically on the request of the user by running 'wmake all' or 'Allwmake'
in the directory as appropriate.