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server: ensure check_config is called during app instantiation

Nicolas Dandrimont requested to merge generated-differential-D7296-source into generated-differential-D7296-target

check_config converts the "stored" configuration (with toplevel keys for most services) into a config suitable for the get_vault function.

Ensure all tests use the same codepath to make sure it is properly exercized, and that the vault backend object can be properly initialized in all cases.

Also contains a couple of refactoring commits to unconfuse the configuration generation via fixtures.

Supersedes !144 (closed)

Test Plan

pytested + tested that the addition of check_config makes the staging deployment happy

Migrated from D7296 (view on Phabricator)

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