Start deleting loose nodes while packing (and commit pack index) in a safe way

[giovannipizzi]

If the dostore container is repacked, typically all objects are first packed, and then one has to call separately the clean_storage function to remove loose objects. However, if the container is big (say 100GB+), this has a high change to end disk space.

One could provide an option to commit the sqlite DB and clean the storage as soon as a pack file is completed, so the additional required space at any time is max ~4GB (and then use it from AiiDA). Pinging @unkcpz as we discussed this together

[giovannipizzi]

As a note, one has to be careful, however to do operations correctly, so there is no risk that a concurrent read process does not find an object at some point in time (eg, one has to commit the sqlite DB and make sure it's written to disk, before attempting any cleaning). Probably calling clean_storage is safe enough, after a commit