fixes random failing ClasspathUpdaterTest

When IJavaProject.setRawClasspath() is explicitly called with
ClasspathEntries distinct from PDE (like in the Test), and then later
PDEs UpdateClasspathJob is executed it can't compute the "oldEntry" and
fails with "... is not on its projects build path". The Message is
correct - it was manually removed from the projects build path. That
state should just be ignored so that PDE continues to set the
IClasspathEntries computed by PDE.

https://github.com/eclipse-pde/eclipse.pde/issues/820