I recently put several old, yucky git directory structures into one new, clean structure in SVN, then pulled the entire SVN repository back out into a new, clean, local git repository. One IntelliJ project was so messed up I had to import the old IntelliJ project, which created a new .iml file having a better name, and deleted the old .iml file. I reconfigured everything, committed back into SVN, and verified other people could open the project and build.
Today I tried to edit a file for the first time in this project and got the message, "These files do not belong to the project". IntelliJ offers to unlock the file or all non-project files in the current session, but both options sound wrong. What have I done to myself, and how do I fix it?
I figured out the problem. The file was still open from before all the shuffling, and was apparently pointing at the original file in its original location! I closed the editor and reopened the file from the project tree without a problem. I hope this helps someone else someday.