If anybody was having a Netbeans Exception (post update to 8.0.1. This would prevent Netbeans from indexing your entire project (atleast thats what happened for me).

The exception could be something like this…

java.lang.NullPointerException
        at org.netbeans.modules.php.dbgp.breakpoints.LineBreakpoint.isValid(LineBreakpoint.java:152)
        at org.netbeans.modules.php.dbgp.breakpoints.LineBreakpoint.refreshValidity(LineBreakpoint.java:145)
        at org.netbeans.modules.php.dbgp.annotations.BrkpntAnnotation.(BrkpntAnnotation.java:63)
        at org.netbeans.modules.php.dbgp.breakpoints.BreakpointAnnotationListener.addAnnotation(BreakpointAnnotationListener.java:105)
        at org.netbeans.modules.php.dbgp.breakpoints.BreakpointAnnotationListener.breakpointAdded(BreakpointAnnotationListener.java:82)
        at org.netbeans.api.debugger.DebuggerManager.fireBreakpointCreated(DebuggerManager.java:883)
        at org.netbeans.api.debugger.DebuggerManager.initBreakpoints(DebuggerManager.java:1055)
        at org.netbeans.api.debugger.DebuggerManager.initBreakpoints(DebuggerManager.java:959)
        at org.netbeans.api.debugger.DebuggerManager.getBreakpoints(DebuggerManager.java:597)
        at org.netbeans.modules.debugger.jpda.projects.BreakpointAnnotationProvider.annotate(BreakpointAnnotationProvider.java:149)
        at org.netbeans.modules.debugger.jpda.projects.BreakpointAnnotationProvider.annotate(BreakpointAnnotationProvider.java:143)
        at org.openide.text.CloneableEditorSupport.ensureAnnotationsLoaded(CloneableEditorSupport.java:392)
        at org.openide.text.CloneableEditorInitializer.initAnnotations(CloneableEditorInitializer.java:640)
        at org.openide.text.CloneableEditorInitializer.run(CloneableEditorInitializer.java:351)
        at org.openide.util.RequestProcessor$Task.run(RequestProcessor.java:1423)
        at org.openide.util.RequestProcessor$Processor.run(RequestProcessor.java:2033)

The best way to resolve it is remove the Netbeans cache. I simply deleted the “.cache/netbeans” directory.

rm -fr ~/.cache/netbeans