The patch moves all config variables to config-main, config-highlight (for highlight colors), and config-keys (for keys). Keys and highlights are configurable in their respective tabs. Parens and Code Context options are in the Highlighting tab, Format Paragraph configurables are in the General tab. The sections in the main.def file where the options are saved are respective to their tab.

If you want, I can change the modules so they also load from their old location if an overriding option isn't found in main.def . However, I would recommend cleanly breaking from the old extensions, with a notice somewhere of where the new options are.

Changing the behavior of the extensions Tab / System is a separate issue that I think would be best handled after this, as this patch already makes a lot of changes.