As discussed on Gitter, we should consider excluding pages from auto-populated navigation if they are tagged as NOT_IN_NAV within a plugin as part of on_files. Currently, only pages tagged with EXCLUDED are not considered. The solution that @oprypin suggested was to simply change:

... to:

documentation_pages = files.documentation_pages(inclusion = InclusionLevel.is_in_nav)

Current workaround:

1. Set pages that should not be auto-populated to InclusionLevel.EXCLUDED in on_files
2. Set pages that were previously excluded to InclusionLevel.NOT_IN_NAV in on_nav (after population)