flash: Random refactoring#274
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One big command translator was getting unwieldy. Just put the `odgi` and `bedtools` parsers in their own functions.
`ir::Builder` was getting pretty big, so it is now `builder::Builder` instead.
I kept confusing byself by thinking that a `Resource` was the thing itself. That was dubious, but it's totally bogus now that references are decorated with encodings (which apply to a given instruction's use of a thing, not the thing itself).
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Just a few organization things I've been meaning to do.