In intellij 16 there is a section “File name Filter” to exclude an extension use !*.java. You can give more detailed patterns as well for example I use the pattern below to only return .java files except those with a name starting or ending with test.
Pattern: !*test.java,*.java,!Test*.java
In recent versions of Intellij the GUI has been updated a bit but the same still applies see the “File mask” on the top right hand corner see image below:
