Project files appear as excluded and refactoring fails in WebStorm 2025.1

After updating to WebStorm 2025.1, my entire project is suddenly treated as if none of the files are included in the project. This makes it completely unusable for basic tasks such as refactoring or navigation.

Observed Behavior:

  • All project files appear greyed out (as if marked "Excluded").
  • No indexation occurs.
  • Refactoring, code navigation, and even autocomplete fail.
  • No folders are shown as "Source Root" in the Project Structure view.
  • I can’t find any way to manually include the folders again.
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Most probably the .idea files got corrupted, the .iml file and/or the modules.xml are either missing or broken. As a result all the project files are treated as non-project. Deleting and re-creating .idea folder should help:
 

  • close the project
  • remove it from Recent projects list
  • shut down the IDE
  • delete the .idea folder
  • restart, open the project root folder with File > Open
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