Step to reproduce:

• Have a git repo with a submodule checked out
• from another client, remove, commit and push the submodule removal
• from the first client, pull the changes (we have "Use rebase instead of merge by default for tracked branches" On here, not sure if it's relevant or not)

Expected result:
All the files of the submodule are gone if there is no uncommited/pushed change, a warning otherwise

Actual result:
The submodule is gone in SourceTree GUI, but the files are still present on disk. SourceTree does not suggest this files as new files for a commit. This files are hidden in the GUI

Also, the submodule data is still in .git\modules*, and cause trouble if you want to replace a submodule by another with the same name, or simply change the URL.