What is the correct way for an extension to modify an existing config variable (either in another extension or in core). For example, ProofreadPage adds the Index namespace to $wgTemplateStylesNamespaces, or SpecialNamespaces modifies $wgExtraNamespaces and $wgNamespaceAliases. Currently this is done by modifying the globals.
I'm slightly suspecting that this sort of thing shouldn't be done, and actually where there's a need to change config variables then an actual mechanism should be provided for doing that (e.g. a hook).