Splitting up README.md into several documents, all found in the docs folder

[harmonbhasin]

I'm not done as yet, however I'd like some feedback! I've added my notes on where I think each doc is below. Please suggest restructuring or removing documents if you don't think they're helpful.

• README.md - I'm not sure what we should update this to be, we can have a table of contents for the doc, but I'm not sure what else would be helpful, your input here would be useful.
• docs
  • batch.md - I think this is pretty much done.
  • run_validation.md - Near finished, want to clean up summary at beginning before figure.
  • run.md - Near finished, considering putting output files and if so, need to figure out the best way to show it; need to clean up the main summary
  • overview.md: I think this is pretty much done
  • troubleshooting.md: I think this is pretty much done
  • usage.md: Need to clean up the compute resources requirement section.
  • faqs.md: We should have more questions here, but for now, I'm fine leaving it with these questions.
  • developer.md: I think the content is good, but I'll want to rearrange this structure using claude
  • installation.md: I think this looks pretty good.
  • output.md: I think this is near finish, other than adding run_validation
  • index.md: I need to do this, although this shouldn't take long, and it shouldn't block you from looking at the other files, expect this to look similar to run.md

[harmonbhasin]

I probably should have merged this into another branch so that the tests didn't run, but I decided to just shut them of manually so that we don't waste minutes.

[harmonbhasin]

Need to update this description.

[willbradshaw]

Still reviewing, but here are some initial comments on what seem to me to be the most important files

[willbradshaw]

Should we have new users run the test suite? That would be a good way to check that the pipeline works in their hands. But maybe we can't be sure their launcher instance will have enough resources to actually run the test suite?

That actually brings up a different topic: we should probably provide some guidance on what size instance is needed to run the pipeline on Batch. @harmonbhasin do you already do this somewhere?

[harmonbhasin]

There wasn't documentation for run_validation workflow before, do we want to add this for this pull request? @willbradshaw

[harmonbhasin]

@willbradshaw this is ready for you to look at!

[willbradshaw]

A couple minor comments to resolve, then we're good to go!