Currently editing the Implicit Plugin-Dpendencies only seem to work
randomly (e.g. if one change some other property along with the change).

This now do not refresh the full target (what seem to reset the
underlying model and remove the dirty flag before changes are applied)
but only updates the UI so finally these thing appear in the target
file.

Fixes https://github.com/eclipse-pde/eclipse.pde/issues/451