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Mkw issue 313 new#315

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mkw_issue_313_new
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Mkw issue 313 new#315
mwalte10 wants to merge 5 commits into
mainfrom
mkw_issue_313_new

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Draft of the vignettes for documentation. Have also moved the components that cross cut the languages outside of the leapfrog-r directory per convo with Mantra. Will comment the places where it is useful to have other eyes.

Comment thread docs/development.Rmd
* Set `intermediate` to all 0s.

### State saving
##TODO: Rob this isn't true any more is it?

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Comment thread docs/development.Rmd
After the config files have been modified, you must run scripts/generate in terminal to generate the needed code for compiling.

## Adding a new model variant
##TODO: Rob/Mantra/Jeff could you update this? I'm not familiar with the process of instituting a new variant.

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