Replace embedded json gem with custom code #9
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Fixes #8, but may not be the best fix. I've tested this on a bunch of the built-in examples, and they run fine, both on my laptop (where current master strangely does work, even though it's Ruby 2.3) and on the DAS-5 cluster (where it didn't work, Ruby 2.0)
Maybe it would be better to rely on a system version of the json gem instead of this (not super-well tested, and probably broken on corner cases) custom code, but I'm not sure how widespread a built-in json gem is. At least on my Ubuntu laptop it seems to be there, and also on DAS-5. It could even be standard on ruby 2 for all I know. Should probably try to find that out.
So feel free to not merge, but I thought I should at least suggest one possible fix. (Also, I need to run MUSCLE on DAS-5 :)).