clarify that 'config' and 'options' should only be module-level variables

From the beginning of fdroidserver, the variables config and options have been declared at the module-level. But then, to make things extra confusing, they are sometimes set to global. So it is sometimes possible within a subcommand to have a global and a module-level version. This sucks a lot. These are some clean-ups that move the codebase towards only ever using these variables at the module-level.

This lays the groundwork to entirely separate options from config. Also, config and options should only ever be used from the common module, never from the subcommand modules. And common.read_config() should do nothing at all with options... future work.

Draft because the commits are based on !1466 (merged)