Refreshing project files

I have to work with multiple branches of our company code. To prevent the need to have multiple projects, I use NTFS junction points that point to the current branch I'm working with. My directory structure looks as follows

projects
branch1
branch2
branch3
project <-- NTFS junction pointing to a branch

I keep my IDEA project files in a subfolder under the branch so that i can reuse them. The problem I have is, when I switch branches the file changes are not all detected by IntelliJ even when I restart the IDE. It slowly detects changes as I navigate to various folders. Is there not a way that I can just tell IDEA: "clear out your caches and reload the whole darn project"

Omair

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Wouldn't it be a lot easier to have multiple projects? Disk space is very cheap, messed up code repository data is not.

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