JIBDE-12860 - JAX-RS validation problems are not linked

Fixed the problem where some markers would not be removed from the resource to be validated between
two validation calls, which meant that duplicate markers for the same problem would exist on each
resource.

Also refactored a bit the search/element retrieval: the JaxrsElementIndexationDelegate now not only
deals with the Lucene indexation and searches, but also uses the metamodel to return collections of
JAX-RS elements, Endpoints or workspace Resources. Although this does not break the public API, the change
from List/Set to Collection impled a few changes in the JUnit tests as well.

Added JUnit tests to covers the fixes.

This patch also fixes:
- JBIDE-15662: Warning Multiple JAX-RS Activators doesn't disappear
- JBIDE-15664: Application path configured in web.xml causes warning