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
There are more gloabal validation parameters. You can suspend all validation (or only the ones you don't need) by going to:
Window > Preferences > Validation.
Here, check the box "Suspend all validators".
Alternatively, uncheck the validators you don't need from the list below.
A full build will be requested which might take some time. But Eclipse will run a lot faster afterwards [But without validation of course]
http://www.flickr.com/photos/jesuspresley/5094048124/