Fix: Prevent duplicate AMRFinderPlus database paths

[jakobnissen]

This PR contains four fixes to AMRFinderPlus and its database manager, fixing three separate bugs. They are made as three separate commits which can be reviewed independently.

The background is that we experienced AMRFinderPlus job failures. The executed command-line contained the option --database '/users/data/Services/galaxy/server/tool-data/amrfinderplus-db/amrfinderplus_V3.12_2024-05-02.2,/users/data/Services/galaxy/server/tool-data/amrfinderplus-db/amrfinderplus_V3.12_2024-05-02.2', which is a bug (note it's the same path, joined with ,)

The underlying issue is that the data manager (DM) would add new rows to the output .loc file every time it was invoked - including if new versions of the data manager was installed. This would result in identical rows in the .loc file.
Then, AMRFinderPlus itself would query that database with <filter type="static_value" value="3.12" column="db_version"/>, which could erroneously result in multiple values being selected.

We fix this here in four steps:

1. Make AMRFinderPlus resistant to multiple identical rows by adding a unique_value filter when querying the database (and test it).
2. Making the AMRFinderPlus DM reentrant, by making it check for pre-existing entries in the database and not add new entries if the entry it wanted to add already existed. This approach was copied from the Nextclade data manager. I include both this fix and the above because users might run an older version of the tool with a new version of the database manager or vice versa; so a fix on both ends will be necessary for some.
3. (implemented with 2 for ease) Add missing db_version column to the DM output, which did not conform to the schema. This is a separate bug.
4. The current tests for the data manager tests the data version 4, which requires AMRFinderPlus v4. However, this has not been released as a tool yet, so these tests fail. Disable v4 in the data manager's tests. Note that this is a third bug in the test suite not related to these other changes. I include it here, because otherwise CI fails.

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