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The best way to keep a program properly indented is to use Emacs to reindent it as you change it. Emacs has commands to indent properly either a single line, a specified number of lines, or all of the lines inside a single parenthetical grouping.
U.3.1 Basic Program Indentation Commands Indenting a single line. U.3.2 Indenting Several Lines Commands to reindent many lines at once. U.3.3 Customizing Lisp Indentation Specifying how each Lisp function should be indented. U.3.4 Commands for C Indentation Extra features for indenting C and related modes. U.3.5 Customizing C Indentation Controlling indentation style for C and related modes.
Emacs also provides a Lisp pretty-printer in the library
This program reformats a Lisp object with indentation chosen to look nice.