Repository creations operations are currently recorded in the
transaction manager at commit time. However, it's not the
transaction manager's responsibility to record the operations
the transactions are doing. Previously we didn't expose methods
on the transaction to do this in the handlers. Now we do, so
move ove the repository creations to be  recorded as part of
repoutil.Create which is used everywhere to create the repository.
This simplifies both transaction manager and makes it easier to
move other operations out from transaction manager.

We also do a full repack prune unreachable objects out from the
repositories. This was done in the transaction manager prior to
moving the recording operations out. The purpose is to ensure
all objects have their dependencies satisfied. Git only guarantees
the connectivity of reachable objects but not the unreachable ones.
Now that the handlers are recording the creations, they need to
ensure the repository is in its final shape before we log the files.

Full repacking is the existing behavior so we keep things as they
are for now. In reality, full repacking is not necessary if we just
walk all introduced objects to ensure their dependencies are met.