FileRepo: fix dirty tracking

Signed-off-by: Ferry Huberts <ferry.huberts@pelagic.nl>
FileRepo: run refresh for the rebuild action

Signed-off-by: Ferry Huberts <ferry.huberts@pelagic.nl>
FileRepo: putArtifact: put the correct file into the index

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