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[devel] Fix running doc_check test and fix all Sphinx warnings

Chris Burr requested to merge cburr/LHCbDIRAC:fix-docs into devel

Many of the fixes were made with: https://pypi.org/project/docformatter/

This PR is going to fail pycodestyle but I don't want to mix code changes into this PR given how big it is.

Edited by Chris Burr

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