Fix directory structure throughout #249
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Update the data management lecture with the new directory structure, so that only that is mentioned (plus Snakemake/Nextflow variants). This removes the mention of the old `NBISweden/project_template` structure, as it does not adhere to what was discussed in issue #247.
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This PR fixes the directory structure according to discussion in #247. Data is put in
data/, results inresults/orresults/<software>/, as applicable. Attempts have been made to change mentions of the old structure as well as to alter wording to fit, but it's possible that something will have slipped through, which testing will hopefully catch.