Enhancing Refreshable.refresh() in repositories.

Adding implementation to AbstractIndexedRepo. Indexes are now regenerated.
LocalIndexedRepo now actually regenerates indexes.
FileRepo refreshes whether or not it was dirty. (previously it only refreshed if it wasn't dirty)
Merge remote-tracking branch 'derheld42/refreshindex'

* derheld42/refreshindex:
  Enhancing Refreshable.refresh() in repositories.
Some minor fixups of the previous commit

Signed-off-by: Ferry Huberts <ferry.huberts@pelagic.nl>