from_disk: only build a model object once

Before this change, a Directory object was built to compute the id of
we fed to the Directory object we built for to_model.

We tested this change on simple information of the Mercurial loader,
with a noop-loader stockage:

swh loader run mercurial https://foss.heptapod.net/mercurial/mercurial-devel directory=/data/repos/mercurial-devel

Median time of 3 run

before: 17 minutes 48 seconds
after: 12 minutes 59 seconds

On a profile of the same run, the to_model call of the from_disk's Directory class took the following percentage:
before: 43%
after: 24%