I have the (mis)fortune of having a large project source-base in which I am working primarily on PHP and JavaScript. I have to have the full project area as the project root
I used to exclude resources from validation via project specific Exclude Group (as the most answer here suggests). But in case anyone is still having problems with disabling validation for a specified folder in 2014 - just mark the folder resource as Derived:

This should disable validation for that folder.
If you are using EGIT you might also want to disable automatic inclusion of derived resources in .gitignore:
