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They should each "do" one thing -- not necessary for each individual change, but helpful for each "group" of changes
Commit messages should indicate what done by commit
Lots of small commitments lead to a steady relationship with your code
"Think a little about what you're doing"
Git doesn't track creation/deletion of empty subdirectories, but it will track adding, deleting, and changing the files within them (it tracks files recursively)
A soft reset is recommended -- gets rid of commits but doesn't change files back
Hard reset -- what it sounds like-- that part of the version history is gone
Branching can be helpful for testing or working parallel
Merge a branch back to master ("trunk") once testing is complete