Clean up timeouts

[RagnarGrootKoerkamp]

• There is the global program timeout for generators/visualizers/building (i.e.anything not submissions), which defaults to 30s and is overridden by --timeout for e.g. bt generate
• There is a per problem submission timeout, which is derived from the timelimit and overridden using --timeout on bt run.

This makes for some inconsistency because now timeout is both a program and problem property.

We could 'fix' the code and always make timeout a program property, which is either derived from the global timeout or from the problem timeout, but I'm not sure that's actually worth fixing.

I think we should fix the duplicate --timeout flag name, since this makes bapctools.yaml configuration a bit annoying otherwise. I'm not exactly sure how though. One option is to give a different name to one of them, but have -T as shortcut for both anyway. (-t is currently the shortcut for timelimit already.)

[mpsijm]

(duplicate of #165)

[RagnarGrootKoerkamp]

Whoops; hitting ctrl-enter instead of enter twice does this. #blamegithub