Create a config.ini (warning it will overwrite an existing config.ini)
using roundup-server -S. Edit the file adding tracker and customizing 
values. Rerun roundup-server -S. No tracker settings or config values
are preserved.

They should all be preserved.

If you use roundup-server -S -C c.ini settings are preserved.

Maybe make roundup-server -S check for config.ini and refuse to
save. It should recommend using 'roundup-server -S -C config.ini'.

Maybe make sure that config.ini has the right keys so we don't
let the user clobber their tracker's config.ini using -C. Maybe
add a [main] magic_number=roundup-server value that is mandatory?