Remove executables from the repo.

These executables require the application bootstrapping that is not
found in this repo, hence they are pretty useless.
Remove -app, -working, and -root parameters.

These legacy parameters are not needed now that we are not supporting
globally installed CakePHP libraries. Because CakePHP will only be
supported in local per application installations, we have far less work
to make paths and environment data consistent and proper.
Remove unused property.
Add exit instructions to ServerShell.
Merge pull request #3340 from markstory/shell-cleanup

3.0 Shell cleanup pt.1