Are there any command line (not interactive, not web-based) tools that will reformat (pretty-print) PHP and Javascript code?
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PHP_ Beautifier is very outdated! For a more modern approach try php-cs-fixer
Example command:
php-cs-fixer fix --rules=@PSR2 path/to/php/src
A second alternative is PHP_CodeSniffer
Example command: phpcbf --standard=PSR2 path/to/php/src
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For a PHP beautifier, you can also use this pear package PHP_Beautyfier, which can either be called from the command line or instantiated within your own PHP code. For the Javascript one instead, find an open discussion here

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Andrea Fiore
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I wrote an article explaining how to build a command-line JavaScript beautifier implemented in JavaScript. The best part - it takes under 5 minutes to do it, YMMV.
Cheers!
Shonzilla