JBIDE-18453 - NPE while processing change in code

Remove a block where the signature of the Java methods were collected but not used
(a remaining of a previous refactoring)
Added some 'waits' in the unit tests (with a bit of API refactoring in the test utility classes) because
some tests would fail with ConcurrentModificationException on maven (some elements would still be processed
in a separate thread when doing the test assertions)