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
Solution.
Go configure what's displayed in the Problems View like lothar proposed, create new custom filter and in "Scope" area choose "On working set". Now press the button right below this option to configure what working set would it be: in working set selection pop-up hit the "New" button and mark all your project files EXCEPT those you want to exclude from validation. You might want to save this working set under convenient name, like "No_Validation_Set".
Summary: 1) working set excluding problematic files. 2) custom Problems View filter to operate on this set.
Issues: when adding new files to project you need to update your working set, so they are validated too.