ui cleanup and scaleable images in greenhouse gas interactive
remove argument parsing from script/setup.rb

Not working yet and causing a problem running:

  script/build-and-deploy-jars.rb --maven-update

and

  cap -T
cap: new tasks: checkout, bundle_install

checkout:
checkout branch and force reset to origin/branch
cap: make sure /var/www/app/tmp exists

needed to run deploy:restart which restarts Passenger
Update DNA interactives + fix minor bugs

[#51414465] [#50672065] [#50746215]
Update "Modeling Transcription" interactive
fix volume calculation and change language in pressure equilibrium interactive

[#49553619]
Push protein slightly towards right side during translation

to avoid collision with amino acid incoming with tRNA.
Update transcribe-step-by-step button

Make it animate to first step if before first step.
Update layouts to center buttons under model
update about text for DNA models
Fix "DNA to Protein" interactive layout
Move logic of "transcribe step by step" to Scripting API from JSON
Major refactoring and optimization of DNA rendering

[#51638559] [#51160333]

Various things are changed. The most important one is that now DNA
nucleotides are added and removed dynamically to / from DOM when
viewport is changed. So only minimal number of nucleotides stays in
DOM. That causes that D3 data binding no longer takes so much time, as
well as overall performance is much better due to simpler DOM tree
structure.

Now DNA can be as long as 500 or even more. Scrolling over DNA and
animations should be smooth. Only MD2D engine can be limiting while it
would have to simulate a few hundreds of amino acids.
Fix a bug connected with incorrect DNA region update

[#51638559]