PR2: Fix spelling errors and add things to dictionary.txt

[cansavvy]

Purpose:

The second PR mentioned on #239 where I fix all the spelling errors and add the words to the dictionary.txt that we need.

As a side consequence, softwares (#244) and ID (#243) and Rmd -> .Rmd inconsistencies have been resolved and added to the CONTRIBUTING.md if they were not previously there.

Closes #243
Closes #244
Closes #239

Strategy

A lot of iterations of running spell check, searching in the project for where those words occurred and determing whether they were legit words and should be added to the dictionary.txt or if they were legit errors and in that case I fixed them.

For non-updated notebooks that had manual citations eg. Yaari et al, _PLoS_ I deleted those because they will be done automatically, but I kept the paper links so that when we do get to updating that notebook we know what the paper and its reference should be.

Unfortunately spelling::spell_check_files() isn't great with hyphens so you will note I put fake words like vivo even though I really wanted it to put in-vivo but it would not take that.

For reviewers:

I wouldn't worry about examples that have not been updated yet. I've basically made them so they will pass but they will be further refined when we get to those examples. I would mostly take a look at dictionary.txt and CONTRIBUTING.md and see if that makes sense, as well as the spelling fixes you will see sprinkled throughout.

Docker/Snakemake rendering components

• In the Docker container, snakemake was run for rendering.

[jashapiro]

I made a number of suggestions to the spelling dictionary, which are best addressed individually below.

I also have a couple of higher level questions about how the spellcheck actually works: do we need plurals in cases of words like "subtype", or does adding that give us "subtypes" for free (if I wrote a spellchecker...I am not sure which decision I would make). Similarly, possessives: if we have "dataset", do we need "dataset's"?

[cansavvy]

Shouldn't this be a proper reference with @Tag (or is this a not-yet-updates page and we don't need to worry about it?)

This module has not been updated yet. (#215) My changes to not yet updated modules are basically just to make the spell check happy for now.

[cbethell]

Looks good and everything checks out! Just one question re running the spell check script locally (it worked fine once I got the package installed, see below for more details!).

[cbethell]

LGTM! 🚀