Bug 63883 Cannot configure option for enabling/disabling exclusion filters or custom output folders on a per project basis
Build M9 JDT/Core supports setting enablement for exclusion patterns and custom output folders on a per project basis. This isn't surfaced in the UI. There is only a global flag in workspace preferences.
org.eclipse.jdt.ui/ui/org/eclipse/jdt/internal/ui/preferences/NewJavaProjectPreferencePage.java
private static IClasspathEntry getJREVariableEntry() {
		return JavaCore.newVariableEntry(new Path("JRE_LIB"), new Path("JRE_SRC"), new Path("JRE_SRCROOT")); 
	}	
	/*
	 * @see IWorkbenchPreferencePage#init(IWorkbench)
	 */
	public void init(IWorkbench workbench) {
	}		
	
	/**
	 * @see PreferencePage#createControl(Composite)
	 */
	public void createControl(Composite parent) {
		super.createControl(parent);
		WorkbenchHelp.setHelp(getControl(), IJavaHelpContextIds.NEW_JAVA_PROJECT_PREFERENCE_PAGE);
	}	
	private Button addRadioButton(Composite parent, String label, String key, String value, int indent) { 
		GridData gd= new GridData(GridData.HORIZONTAL_ALIGN_FILL);
		gd.horizontalSpan= 2;
		gd.horizontalIndent= indent;
		
		Button button= new Button(parent, SWT.RADIO);
		button.setText(label);
		button.setData(new String[] { key, value });
		button.setLayoutData(gd);
		button.setSelection(value.equals(getPreferenceStore().getString(key)));
		
		fRadioButtons.add(button);
		return button;
	}