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If the "Store generated project files under project root" option was enabled, IDEA didn't store a flag indicating that a library, an artifact, or a facet was imported. So this information was lost when the project was reopened, and this led to incorrect behavior (e.g. IDEA doesn't show a warning if a user tries to edit imported configurations). Also, if the option to store generated project files under project root was switched off, such generated files weren't always removed from .idea. GitOrigin-RevId: 97b572b6b6ee080c8a33d6424e8c01cb7a041c25