Also don't add 'final' everywhere. I think that's probably a little overzealous and intrusive.

dmyersturnbull · dmyersturnbull · commit dbd1f9f62dd4 · 2013-08-09T14:30:39.000-07:00
diff --git a/development/eclipse/biojava-cleanup.xml b/development/eclipse/biojava-cleanup.xml
@@ -13,7 +13,7 @@
 <setting id="cleanup.remove_unused_private_members" value="false"/>
 <setting id="cleanup.never_use_parentheses_in_expressions" value="true"/>
 <setting id="cleanup.remove_unnecessary_casts" value="true"/>
-<setting id="cleanup.make_parameters_final" value="true"/>
+<setting id="cleanup.make_parameters_final" value="false"/>
 <setting id="cleanup.use_this_for_non_static_field_access" value="true"/>
 <setting id="cleanup.use_blocks" value="true"/>
 <setting id="cleanup.remove_private_constructors" value="true"/>
@@ -24,19 +24,19 @@
 <setting id="cleanup.add_default_serial_version_id" value="true"/>
 <setting id="cleanup.make_type_abstract_if_missing_method" value="false"/>
 <setting id="cleanup.qualify_static_member_accesses_through_subtypes_with_declaring_class" value="true"/>
-<setting id="cleanup.make_variable_declarations_final" value="true"/>
+<setting id="cleanup.make_variable_declarations_final" value="false"/>
 <setting id="cleanup.add_missing_nls_tags" value="false"/>
 <setting id="cleanup.format_source_code" value="true"/>
 <setting id="cleanup.add_missing_override_annotations" value="true"/>
 <setting id="cleanup.qualify_static_method_accesses_with_declaring_class" value="false"/>
 <setting id="cleanup.remove_unused_private_types" value="true"/>
-<setting id="cleanup.make_local_variable_final" value="true"/>
+<setting id="cleanup.make_local_variable_final" value="false"/>
 <setting id="cleanup.add_missing_methods" value="true"/>
 <setting id="cleanup.add_missing_override_annotations_interface_methods" value="true"/>
 <setting id="cleanup.correct_indentation" value="true"/>
 <setting id="cleanup.remove_unused_imports" value="true"/>
 <setting id="cleanup.remove_trailing_whitespaces_ignore_empty" value="false"/>
-<setting id="cleanup.make_private_fields_final" value="true"/>
+<setting id="cleanup.make_private_fields_final" value="false"/>
 <setting id="cleanup.add_generated_serial_version_id" value="false"/>
 <setting id="cleanup.organize_imports" value="true"/>
 <setting id="cleanup.sort_members_all" value="false"/>
