I've been doing some testing and right now if you change a file outside of the idea (through a text editor or through a version control update), when you switch back to IntelliJ it automatically uploads the file to Salesforce.
We would like it to not do this, or have a way to turn this off at the project level. The scenario where this causes problems is:
- Developer 1 is working updates to file A which is checked in to source control in org A, but hasn't checked their changes in yet.
- Developer 2 is refreshes their files from source control to start working on file B. When they switch back to IntelliJ, file A is uploaded and overwrites the changes developer 1 was working on (or worse: updates checked in to another branch).
Ideally IntelliJ should only upload files if the file is saved from within IntelliJ itself, or the user explicitly tells it to upload.
Unfortunately our business model is such that each developer does not get their own org, since we're dependent on our clients to provide development orgs for us.
I created this as a "blocker" priority since this same issue is the main reason we don't use the Force.com IDE either. Feel free to change it.