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Replace deprecated options with a config file override in cli tests

Nicolas Dandrimont requested to merge generated-differential-D2805-source into generated-differential-D2805-target

This paves the way for removal of all the deprecated cli options in swh journal.

Depends on !127 (closed)

Test Plan

tox tests updated, again

Migrated from D2805 (view on Phabricator)

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