Fix project structure disappearing intermittently

Problem

• After opening a project, the ide just constantly indexes and scans the project, which causes the project packages to disappear and re-appear in the project tree.

• The project structure intermittently disappears and reappears upon opening.

• The project vanishes from the project view when I switch the window

• Issue is commonly observed when the project is in macOS's Documents directory.

• Logs indicate "java.nio.file.FileSystemException" for the project path.

  14 Jul 2025 09:54:52,975 WARN — #c.i.o.v.i.l.LocalFileSystemBase — /Users/username/projectpath: Operation not permitted
  java.nio.file.FileSystemException: /Users/username/projectpath: Operation not permitted
  	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
  

Cause

The issue is likely due to restricted file access permissions on the directory where the project is stored. This might prevent IntelliJ IDEA from properly reading or maintaining the project's configuration files, resulting in the behavior.

Resolution

1. [Optional] Relocate the Project:

   • Move the project folder to a directory where IntelliJ IDEA has unrestricted read and write access. For example, avoiding locations like the Documents folder can prevent access-related permissions from interfering. Please check the log for the path where IDEA could not perform the operation.

2. Allow Disk Access for IntelliJ IDEA:

   • Navigate to your system's security settings: System Settings > Privacy & Security > Full Disk Access.
   • Enable full disk access for IntelliJ IDEA. You might need to add it manually by clicking on the (+) button, locating the IntelliJ IDEA application, and adding it.
   • To allow access only to specific locations instead, go to System Settings > Privacy & Security > Files & Folders and turn on access to the project location (for example, Documents) for IntelliJ IDEA.

This issue has been reported in IDEA should notify users on macOS if there is no access to the directory of the project and require access (IDE project files disappear and reappear, or fail to show any files due to permission issues) . Please subscribe to it for further updates.