When using Git with IntelliJ IDEA, pressing Ctrl+K (for VCS Commit Changes...), it shows that what it's about to commit are all the changes, not just what's in the index.
I couldn't seem to find anywhere where it's possible to commit only the index so as of now I'm forced to use CLI's git commit command without -a to commit only the index.
By the way if you do a Stash within the IDE, it does give you a checkbox for whether you want to keep the index, so there is an example of the use of indexes in the IDE.
How can committing be done by only committing the index?
This feature is available as of 2020.3 (Docs, Issue: IDEA-63391).