As far as I know, the only way to exclude a directory is to mark it as excluded in project structure. However, this would make IntelliJ totally ignore the directory. Thus it will not appear in autocomplete options.
I do not want this. I want exclusion from inspections but inclusion in everything else. Is this possible?
I'm using Intellij 12.0.2. And, it's actually the bootstrap css and js failing the inspection.
As suggested by Peter Lawrey, the proper solution would be to use the custom inspection scope that excludes the directories where you don't want the inspections to be run.