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
addComboBox(othersComposite, label, PREF_PB_DUPLICATE_RESOURCE, errorWarning, errorWarningLabels, 0);
		String[] errorWarningIgnore= new String[] { ERROR, WARNING, IGNORE };
		
		String[] errorWarningIgnoreLabels= new String[] {
			PreferencesMessages.getString("CompilerConfigurationBlock.error"),  
			PreferencesMessages.getString("CompilerConfigurationBlock.warning"), 
			PreferencesMessages.getString("CompilerConfigurationBlock.ignore") 
		};
		label= PreferencesMessages.getString("CompilerConfigurationBlock.pb_check_prereq_binary_level.label");  
		addComboBox(othersComposite, label, PREF_PB_INCOMPATIBLE_JDK_LEVEL, errorWarningIgnore, errorWarningIgnoreLabels, 0);	
		label= PreferencesMessages.getString("CompilerConfigurationBlock.build_invalid_classpath.label"); 
		addCheckBox(othersComposite, label, PREF_BUILD_INVALID_CLASSPATH, abortIgnoreValues, 0);
		label= PreferencesMessages.getString("CompilerConfigurationBlock.build_clean_outputfolder.label"); 
		addCheckBox(othersComposite, label, PREF_BUILD_CLEAN_OUTPUT_FOLDER, cleanIgnoreValues, 0);
		
		description= new Label(othersComposite, SWT.WRAP);
		description.setText(PreferencesMessages.getString("CompilerConfigurationBlock.resource_filter.description")); 
		gd= new GridData(GridData.FILL);
		gd.horizontalSpan= nColumns;
		gd.widthHint= fPixelConverter.convertWidthInCharsToPixels(60);
		description.setLayoutData(gd);
		
		label= PreferencesMessages.getString("CompilerConfigurationBlock.resource_filter.label"); 
		Text text= addTextField(othersComposite, label, PREF_RESOURCE_FILTER, 0, 0);
		gd= (GridData) text.getLayoutData();
		gd.grabExcessHorizontalSpace= true;
		gd.widthHint= fPixelConverter.convertWidthInCharsToPixels(10);
		
		return othersComposite;
	}