I was worried about the same problem, I just wanted to unite, not worrying about non-content changes.
I found out that (in IDEA 2016.2) you can compare differences between projects (folders) instead of version differences. It even provides a good graphical overview of additions and abstractions based on content rather than data versions.
- Check both branches
- Open the branch you want to join with in IDEA
- Select the base folder you want to merge (possibly the entire project folder) and press ctrl + D (Compare with ...)
Now you get a much more complete window with all the changes and filtering options. You can even decide how to compare intelliJ (content, date, ...)
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