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fix various small issues

Alex Kanitz requested to merge various_fixes into master
  • remove log files and add '.snakemake' directories to '.gitignore'
  • update wrong link in 'README.md'
  • delete superfluous script documentation 'scripts/labkey_api.md'
  • add Snakemake-specific file extension '.smk' to subworkflows
  • remove non-deterministic workflow output from md5 sums

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