[launching] The run configuration clean overrode -runkeep

The  Run configuration specifies a clean option. This caused the setting of the -runkeep to be discarded. Will now only look at it when the -runkeep is off. Also removed the cleaning of the directory since this happens in the launcher.

Example of doing things in two places. This kind of stuff must only be done in bnd!
Merge pull request #985 from pkriens/master

[launching] The run configuration clean overrode -runkeep