My project in Version Control -> Directory Mapings has 4 git repositories defined
(main repo + 3 plugin repos in /plugins directory)
If you want to replicate directory structure see CakePHP Application Skeleton
After right clicking on commit (for example 3a5e950d99558210abe9f493e880ef0a5d0ab3a7) and selecting Use commit as Git Scope invalid scope is created of
3a5e950d99558210abe9f493e880ef0a5d0ab3a7, 3a5e950d99558210abe9f493e880ef0a5d0ab3a7, 3a5e950d99558210abe9f493e880ef0a5d0ab3a7, 3a5e950d99558210abe9f493e880ef0a5d0ab3a7