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There are several bugs in how MonoDevelop handles folders in projects. Here are some ways issues can be triggered:
1) Add a new folder. An explicit reference to the folder is added to the csproj as the folder is empty. Add a file to it using the 'Add New File' dialog. An explicit reference to the folder is maintained in the csproj. Drag the new file out of the folder into another folder (or project root). Another explicit reference is added.
2) The same as '1' except use the 'Add existing file' dialog
3) The same as '1' except drag a file into the folder from somewhere else
Similarly, if the last file is removed or deleted from a folder, an explicit reference is not added to the csproj to ensure the folder is persisted.
Note: You may need to rename the directory for this to have a visible effect, but i end up with issues like this in my csproj: http://screencast.com/t/UhkzFuFpUT
Thanks so much for taking the time to submit this report! I attempted to reproduce this issue based on the bug description with the latest Visual Studio 2017 for Mac Preview version 7.2, and I was unable to hit the problem. If this issue is still occurring for you, please reopen this report and attach a reproduction, ideally starting with a new template project and then adding just the code necessary to demonstrate the issue.