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/CompilerConfigurationBlock.java
private void updateEnableStates() {
		boolean enableUnusedParams= !checkValue(PREF_PB_UNUSED_PARAMETER, IGNORE);
		getCheckBox(PREF_PB_SIGNAL_PARAMETER_IN_OVERRIDING).setEnabled(enableUnusedParams);
		
		boolean enableDeprecation= !checkValue(PREF_PB_DEPRECATION, IGNORE);
		getCheckBox(PREF_PB_DEPRECATION_IN_DEPRECATED_CODE).setEnabled(enableDeprecation);
		getCheckBox(PREF_PB_DEPRECATION_WHEN_OVERRIDING).setEnabled(enableDeprecation);
		
		boolean enableThrownExceptions= !checkValue(PREF_PB_UNUSED_DECLARED_THROWN_EXCEPTION, IGNORE);
		getCheckBox(PREF_PB_UNUSED_DECLARED_THROWN_EXCEPTION_WHEN_OVERRIDING).setEnabled(enableThrownExceptions);
		boolean enableHiding= !checkValue(PREF_PB_LOCAL_VARIABLE_HIDING, IGNORE);
		getCheckBox(PREF_PB_SPECIAL_PARAMETER_HIDING_FIELD).setEnabled(enableHiding);
		
		boolean enableJavadoc= checkValue(PREF_JAVADOC_SUPPORT, ENABLED);
		fJavadocComposite.setVisible(enableJavadoc);
		boolean enableInvalidTagsErrors= !checkValue(PREF_PB_INVALID_JAVADOC, IGNORE);
		getCheckBox(PREF_PB_INVALID_JAVADOC_TAGS).setEnabled(enableInvalidTagsErrors);
		setComboEnabled(PREF_PB_INVALID_JAVADOC_TAGS_VISIBILITY, enableInvalidTagsErrors);
		
		boolean enableMissingTagsErrors= !checkValue(PREF_PB_MISSING_JAVADOC_TAGS, IGNORE);
		getCheckBox(PREF_PB_MISSING_JAVADOC_TAGS_OVERRIDING).setEnabled(enableMissingTagsErrors);
		setComboEnabled(PREF_PB_MISSING_JAVADOC_TAGS_VISIBILITY, enableMissingTagsErrors);
		
		boolean enableMissingCommentsErrors= !checkValue(PREF_PB_MISSING_JAVADOC_COMMENTS, IGNORE);
		getCheckBox(PREF_PB_MISSING_JAVADOC_COMMENTS_OVERRIDING).setEnabled(enableMissingCommentsErrors);
		setComboEnabled(PREF_PB_MISSING_JAVADOC_COMMENTS_VISIBILITY, enableMissingCommentsErrors);
	}
	private IStatus validateCompliance() {
		StatusInfo status= new StatusInfo();