(1/5) Rearrange software docs: Using renv

[sjspielman]

Towards #458

This is the first of several ("pseudostacked"!) PRs to break up the current software page. Note the updated scheme for this plan in https://github.com/AlexsLemonade/OpenScPCA-analysis/issues/458#issuecomment-2150560957

This PR adds the following:

• Initializes a reproducibility directory (just a stub index for now)
• Initializes a managing software directory with an index.md. This file is wholly new.
• Ports renv software content into a new file using-renv.md in the managing software directory. There are a few rephrasings here that I noticed, but no "big" changes besides the occasional updated wording.

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Here's what you can expect for the additional PRs to close out this issue:

• A PR to add a using-conda.md doc
• A PR to add a reporting-dependencies.md doc
• [EDIT: this step added] A PR to add the primer page for #498 (since this will affect relative links 👇 )
• After all of the above (including this PR) go in, I'll file a PR which removes the original software dependencies doc, updates the mkdocs.yml file to match the current set of software files, and fixes all the relative links that break after the mkdocs.yml change 🎢
  • I will likely also add some relative links to the documenting-your-analysis.md page that points to a lot of these changes

[sjspielman]

Just a few style comments, one of which is a type that would have been caught with running on spellcheck on the branch... so I'm wondering if setting that up is something we want to do?

That is currently hanging out in #503, but I can add that change in here too. Can't hurt, it's a small enough change to have "in parallel"!