Delete inactive configurations.

Doing nothing when doDelete() method is called on MatrixProject causes that configuration which was requested to be deleted by its delete() method is deleted from disk, but kept in memory in state disabled. This causes problems.
I am glad to hear you use NetBeans :-) but please make sure new files have license headers. (Normally this should be automatic, because `pom.xml` does specify `<licenses>`; you might however be running an older version of the IDE that does not recognize `http://opensource.org/licenses/MIT`, only `http://www.opensource.org/licenses/mit-license.php`.)