Collections do not appear in "Navigation" tab (or after very long delay - or mysterious action(s)?)
The following message appears frequently in Navigation tab: generally, collections appear after a while (and/or reloads), but the delay can be very long - up to several minutes - and unpredictable (which action makes them appear?)
It is easy to reproduce with a big project: try to "Git clone" Joram ( https://gitlab.ow2.org/joram/joram.git ) in the GIT manager, then see what happens. Screenshot below: