[INTERNAL] Separate business logic from helper logic in FileListDiff

The methods were split in parts necessary for the return values and in
mere side-effects. Since the side-effects completely rely on the return
values, they were simply moved to the only caller
(IncomingProjectNegotiation).

Change-Id: I650bcccef68b6c1bbccc7738a0a5b3a8b21c4740
Reviewed-on: http://saros-build.imp.fu-berlin.de/gerrit/1556
Tested-by: Jenkins CI
Reviewed-by: Franz Zieris <zieris@inf.fu-berlin.de>