task-based execution user guide edits

[atravitz]

Description

documentation notes from @hannahbaumann addressed in this PR:

• Since the vocabulary of tasks and task-based execution will be new to a lot of our users, it would be great to introduce them in the user guide.
• This part in the user guide is confusing, since the default alchemical network output file name is alchemicalNetwork.json, but here we're switching to tyk2.json, even though the paragraph above says the output is alchemicalNetwork.json.

  Once you have an AlchemicalNetwork, use the following command to set up the task-based campaign. By default, the TaskDB and Warehouse will be created using the input file basename (here, tyk2).

• Re parallel submission of multiple jobs: I think here we could also mention the use of array jobs, e.g. sbatch --array=1-100 run_tasks.sh which would make parallel execution more practical then manually submitting the same job many times.
• Maybe the user guide could also briefly explain where run-task stores the results? (including the shared and scratch directories?)

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Checklist

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Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).

• GPU integration tests
• example notebook testing
• packaging tests: run this for any large feature PRs or PRs that add test data.

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