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(composite, label, PREF_PB_INVALID_JAVADOC_TAGS_VISIBILITY, visibilities, visibilitiesLabels, indent);
		label= PreferencesMessages.getString("CompilerConfigurationBlock.pb_invalid_javadoc_tags.label"); 
		addCheckBox(composite, label, PREF_PB_INVALID_JAVADOC_TAGS, enabledDisabled, indent);
		Label separator= new Label(composite, SWT.HORIZONTAL);
		gd= new GridData(GridData.HORIZONTAL_ALIGN_FILL);
		gd.horizontalSpan= nColumns;
		separator.setLayoutData(gd);
		
		label = PreferencesMessages.getString("CompilerConfigurationBlock.pb_missing_javadoc.label"); 
		addComboBox(composite, label, PREF_PB_MISSING_JAVADOC_TAGS, errorWarningIgnore, errorWarningIgnoreLabels, 0);
		label = PreferencesMessages.getString("CompilerConfigurationBlock.pb_missing_javadoc_tags_visibility.label"); 
		addComboBox(composite, label, PREF_PB_MISSING_JAVADOC_TAGS_VISIBILITY, visibilities, visibilitiesLabels, indent);
		
		label= PreferencesMessages.getString("CompilerConfigurationBlock.pb_missing_javadoc_tags_overriding.label"); 
		addCheckBox(composite, label, PREF_PB_MISSING_JAVADOC_TAGS_OVERRIDING, enabledDisabled, indent);
		separator= new Label(composite, SWT.HORIZONTAL);
		gd= new GridData(GridData.HORIZONTAL_ALIGN_FILL);
		gd.horizontalSpan= nColumns;
		separator.setLayoutData(gd);
		
		label = PreferencesMessages.getString("CompilerConfigurationBlock.pb_missing_comments.label"); 
		addComboBox(composite, label, PREF_PB_MISSING_JAVADOC_COMMENTS, errorWarningIgnore, errorWarningIgnoreLabels, 0);
		label = PreferencesMessages.getString("CompilerConfigurationBlock.pb_missing_comments_visibility.label"); 
		addComboBox(composite, label, PREF_PB_MISSING_JAVADOC_COMMENTS_VISIBILITY, visibilities, visibilitiesLabels, indent);
		
		label= PreferencesMessages.getString("CompilerConfigurationBlock.pb_missing_comments_overriding.label"); 
		addCheckBox(composite, label, PREF_PB_MISSING_JAVADOC_COMMENTS_OVERRIDING, enabledDisabled, indent);
		return outer;
	}