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If a freeform project whose project.dir is external to the nbproject folder was previously opened, when the IDE starts and opens it automatically its project.dir node is missing from the Files tab.
I'm using 6.1M1; P1 since it is a regression (this is mentioned in the guidelines).
Already reported, the dupe issue is P2, because the workaround is simple - reopen the project. *** This issue has been marked as a duplicate of 125839 ***