Keep "Exclude from validation" after project clean
Being able to select a folder, right click and select exclude from options is a great feature. It would be great for it to remain in force a project clean. After a clean, in order to make it take affect again, one needs to uncheck it and then check it again. I think this is also a problem after closing a project and reopening it.

The behavior you describe is how “exclude from validation” is supposed to work already – I ran a few quick tests to confirm this.
If you see contrary behaviour, could you let us know for what file types you are seeing undesired validation on clean?
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Eric Lentz commented
A feature that I enable becomes DISABLED after a clean and that's the way it is supposed to work? Okay, if you believe that's not a bug, that's fine. This isn't a bug report. This is a request to change that functionality so that after a clean the excluded validation CONTINUES to be excluded. That would make MyEclipse more usable, in my opinion.