Allow to change the checkout into single directory by configuration

This pertains to CONTINUUM-2524. If we're going to change the default behavior of checking out a multi-module project into a single directory, user should be allowed to change this behavior by configuration. So that if a user prefers to store each module into a separate working directory, he can do so without the need to explicitly selecting the 'Checkout multi-module project in single directory' radio box when adding the project to Continuum.

See related threads:

http://old.nabble.com/CONTINUUM-1569-and-2193-staged-ts23519500.html
http://old.nabble.com/Merge-branch-for-flat-multi-module-support-to-trunk-ts28592236.html