tests: Reduce the number of warnings raised

TODO

• pytest:
  • Unknown pytest.mark.inbound_message
  • unused pytest asyncio_mode config option
• Converter 'swhid' is already registered
• Vault & Indexer storage DeprecationWarning while init using args
• docutils:
  • frontend.OptionParser is deprecated
  • use Node.findall instead of Node.traverse
• UrlField's default scheme -> transitional setting + silence warning
• Naive datetime value used for an aware field
• Re-implemented GitLoaderFromDisk to remove the last dependency to the deprecated swh.loader.git.from_disk
• Identifying contents by sha1 instead of hash dicts {"sha1": b"..."} is deprecated
• test_message method is not a test

Will be fixed elsewhere

• Commit.extra is deprecated swh-loader-git!189 (merged)
• The 'strip_cdata' option of HTMLParser() has never done anything and will eventually be removed. https://bugs.launchpad.net/beautifulsoup/+bug/2076897

Wontfix here

• warnings related to pybadges: pkg_resources is deprecated in py3.12 (a pr exists to fix this since June) and imghdr in py3.13 (needs an external replacement like filetype)
• warning related to htmlmin: cgi is deprecated and slated for removal in Python 3.13, package is not maintenained anymore, maybe we should switch to its fork https://github.com/wilhelmer/htmlmin or something else (like django-minify-html

Results

Down from 41630 warnings in master to 1185, mostly (1136) due to a deprecation warning fixed in swh-loader-git!189 (merged) 🎉

The only change impacting swh-web behavior is setting https the default scheme for UrlFields (hence the change in e2e tests).