[DOC-1367] Update known issues to include a note about basemodulepath needing to be set in [main]

This patch adds a note to the known isseus page and the upgrade notes
page to inform people that `basemodulepath` needs to be in `[main]`,
and if it is just set in `[master]` it will cause the upgrader to fail

This PR also includes a fix for DOC-1368 as part of this patch