The difference between those three commands can be inferred from their parameters and flags.
Git add .
What does . mean?
That's right. It means the current directory. So, git add . adds all files and folders located in the current directory including hidden files/folders.
Git add -a
-a flag is the shorter version of the --all flag, and as can be inferred it means adding all files and folders, but isn't that what git add . does? Well, you missed "the current directory" part. I know you haven't missed it, smart guy, I am just playing with you .
Getting back to the point, git add -a adds all files or folders in the whole repository, not just the current directory.
So that means if you modified a file in the repo main directory, cd'ed into a sub-directory, modified another file then ran the earlier command git add . you will only add the file in the subdirectory.
git add -u
-u flag is the shorter version for --update flag, and again as can be inferred, it means updating files and folders but there is a caveat, new files/ folders are not tracked,
and thus they can't be updated. So basically that means modified and deleted files/folders are added but not newly created ones.
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