Specifically, these were fixed:

./03-commandline.md:30: MD002 First header should be a top level header
./03-commandline.md:132: MD012 Multiple consecutive blank lines
./03-commandline.md:173: MD012 Multiple consecutive blank lines
./03-commandline.md:317: MD012 Multiple consecutive blank lines
./03-commandline.md:318: MD012 Multiple consecutive blank lines
./03-commandline.md:67: MD031 Fenced code blocks should be surrounded by
  blank lines
./03-commandline.md:151: MD031 Fenced code blocks should be surrounded
  by blank lines
./03-commandline.md:48: MD032 Lists should be surrounded by blank lines
./03-commandline.md:51: MD032 Lists should be surrounded by blank lines
./02-basic-computer-background.md:71: MD002 First header should be a top
  level header
./04-git.md:35: MD002 First header should be a top level header
./04-git.md:153: MD009 Trailing spaces
./04-git.md:341: MD009 Trailing spaces
./04-git.md:262: MD012 Multiple consecutive blank lines
./04-git.md:372: MD012 Multiple consecutive blank lines
./04-git.md:357: MD013 Line length
./04-git.md:109: MD032 Lists should be surrounded by blank lines
./README.md:40: MD012 Multiple consecutive blank lines