add check on 'is dirty' flag

[kafetzakid]

For a successful sync, the method will be more robust if there is an additional check on whether the 'is dirty' flag is set correctly. Currently there is a check on replicas status using check_data_object_replica_status() in upload_to_irods(). However, in do_initial_sync_and_or_restart() the replica status is not checked to infer whether "matched" or "ignored".

[paulborgermans]

is dirty flag is not in PRC, but an internal tool ;-)

do_initial_sync_and_or_restart() has a different purpose: see if the file already exists. If it does not exist, the replica status will be checked after upload. If we add a replica check there and the replicas are not healthy, an upload attempt will very likely fail

So it should be ignored, but reported, likely in a different category

So bottom line: I will add the replica check for existing files and add it to the report data/json