Code formatter / beautifier for bash (in command line)?

you can script vim to do: "gg=G" that means "indent all the file"

You could give shfmt a try. It implements its own shell parser including Bash support, so it's more robust than plaintext-based tools.

And both the parser and printer are available as Go packages, so it should be easy to write a 20-line Go program to manipulate or play with shell code.

Please note that I'm the author, so the advice may be a bit biased :)