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ra: Fix directory removal when processing a commit

Antoine Lambert requested to merge generated-differential-D3889-source into generated-differential-D3889-target

Due to an invalid isinstance type check (swh.model.model.Directory instead of swh.model.from_disk.Directory), the loader ended up with error when a directory was removed in a subversion commit.

Sentry related issue: https://sentry.softwareheritage.org/organizations/swh/issues/2563/?project=14&query=is%3Aunresolved

Test Plan

I added a new test processing a sample repository where a directory is added in a commit and removed in another commit.

Migrated from D3889 (view on Phabricator)

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