Fix docs builds and prohibit warnings again

[unito-bot]

We had to allow warnings in the doc build to get through the rest of CI for the release, but we should fix whatever the underlying problem was and turn the no-warnings check back on.

┆Issue is synchronized with this Jira Story
┆Issue Number: TOIL-1573

[adamnovak]

We turned them off in 6a1bbbd

[adamnovak]

The docs fail to build with sphinx-autoapi 3.1 due to warnings like:

/builds/databiosphere/toil/docs/autoapi/toil/utils/toilStats/index.rst:: WARNING: more than one target found for cross-reference 'TemporaryID': toil.job.TemporaryID, toil.jobStores.fileJobStore.TemporaryID, toil.leader.TemporaryID, toil.test.jobStores.jobStoreTest.TemporaryID, toil.test.src.jobDescriptionTest.TemporaryID, toil.wdl.wdltoil.TemporaryID

The docs see many duplicate copies of things imported by name.

On sphinx-autoapi 3.0 we do not have this problem.