Clear errors and warnings before applying validators so they appear.
Fix NRE when validating a project and no properties file set on builder.
Only override trace setting when it's been set on ILaunchConfiguration.

Otherwise, it's always false even if it's been set in the *.bndrun file
because we end up getting the default value (false) from the
ILaunchConfiguration. This is nice because I rarely use the Debug
Configurations page, and instead rely on the bndrun file to tweak.
When checking deltas for updates use portal paths for run bundle set.

On windows the directory separator difference would cause this to never
return a positive match.