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If I spend the time to create a large number of make targets on a directory, then I need to rename the directory to something else (or copy it) the make targets should move/copy with it. Currently when a directory is renamed, the make targets just dissappear, but then re-appear if I create a new directory using the old name. This is likely not intuitive behaviour and since the set-up cost of make targets is high, it would help to minimize frustration.
There is a workaround: As you might have noticed the make targets are not removed from the .cprojects file (that is why they reappear if you create a new folder with the old name). Thus, you can change the folder name in the .cprojects file manually and have your make targets back. Not very intuitive but it just works.