Bias disclaimer: I am the ChiliProject lead and a former Redmine core contributor.
As far as code and features go: ChiliProject was forked in January so there are quite a few changes between it and Redmine. I'll try to quickly describe how we (ChiliProject) do our releases and what is included in them:
The ChiliProject 1.x releases include:
- Redmine 1.1
- extra bug fixes
The ChiliProject 2.x releases include:
- Redmine 1.1
- some parts of Redmine 1.2
- new features that are only in ChiliProject
- even more bug fixes
If you want details about the exact changes you can check out what was included in our previous versions. I also used Google Spreadsheet to track what I pulled into ChiliProject from Redmine 1.2:
https://www.chiliproject.org/boards/2/topics/239
For the non-code differences (community), the Why Fork? and FAQ pages are the best places too look.
As far as themes and plugin compatibility: they should work with either project at this point. Keeping compatibility is a big focus of mine right now, since I don't want to have to go and update all of my plugins whenever there is a new release of Redmine or ChiliProject.
Hope this helps.
