Patch intellij update

Calling this `patch-` since this is not a feature on the code at all.

Anyway, this updates the project files so they are compatible with the latest release.

See merge request !43

Feature fix logs

Fix for double logs for BiopetQCommandLine

See merge request !42

Feature bump version

see #56

See merge request !40

Feature sharkapps

sample config file, which should be used by everyone during development.

See merge request !41

Feature fix gatk pipeline

Fix some small options on the gatk pipeline

See merge request !39

Feature dirty warns

See #75

See merge request !38

Allele mode now also on discovery alleles