Ensure module options override module-set options for same module.

It has always been the intention since module-set was introduced that it
would be possible to override options set for a module used in that
module-set by making a later module declaration, without that later
module declaration actually changing the build order or making any other
effect. This feature was broken and reported as a bug.

I've added a testcase to reproduce the problem, and I have fixed it by
passing back to parse_module() existing Module objects when present, and
modified parse_module() to not create new Module objects in that case
but to modify the one provided.

I've also added a warning for modules that do not appear to be part of a
module set as this indicates duplicate modules passed in the config
file. As of right now the way this test works is to look for a
module-set name but those are optional, so what I'll probably do is
auto-generate a module-set name based on the line number. That will come
later though.

BUG:288611
FIXED-IN:1.15