[backport 3.0.x-juno] Deprecation warnings no longer accumulate

The reason why that used to happen is that the Eclipse markers attached to the
dependent sources recompiled by Sbt were not removed, and hence the deprecation
warnings (or any other kind of problem marker) were being accumulated after
each incremental build.

The fix consists in deleting all problem's marker attached to a unit when the
unit is about to be parsed. This should really be seen as a workaround until
Sbt provides a better interface for incremental compilation. In fact, ideally
Sbt should provide a notification mechanism to know what is the set of
compilation units that are about to be recompiled, **before** the actual
recompilation step is performed.  Unfortunately, that is not possible at the
moment, hence we are left with the current hack.

Huge thanks to @gkossakowski for suggesting this very effective workaround.

Fixed #1001595

(cherry picked from commit 56e4328e736e5f3aa2e424f741cf80e92e3d1d2b)
(squashed commit 1112d0aefbf01bef9d93db0518aae67bedc5a39d)

Conflicts:

        org.scala-ide.sdt.core/src/scala/tools/eclipse/buildmanager/sbtintegration/EclipseSbtBuildManager.scala
(cherry picked from commit 631f3168c0880b3c184951f8e8f095319eacebd5)