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docs: update and amend simulation stage output file explanations #218

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I came across some inconsistencies and omissions in the docs about simulator.py output files, while creating a snakemake wrapper for nanosim. So here's my attempt to fix this. Feel free to take what you find useful and change whatever I got wrong.

Also, I'll add some more info on metagenome in a commit in a second, just wanted to make sure I don't lose track of the pull request in doing so...

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