Down and Dirty Guide to Installing PHP Mess Detector on OS-X and Integrating with PHPStorm

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Download PHP Mess Detector PHAR

  wget -c http://static.phpmd.org/php/latest/phpmd.phar

Move the PHAR and "install it"

  sudo mv phpmd.phar /usr/local/bin/phpmd
  sudo chmod +x /usr/local/bin/phpmd

Check to make sure it's running on your system
  type phpmd at the command prompt and you should get back a list of Mandatory and Optional arguments

To associate with PHPStorm:

  type which phpmd at the command line and copy the resulting path.

  In PHPStorm
  1) Navigate to Preferences->Languages & Frameworks -> PHP -> Mess Detector and click the ... icon in the Development Environment and paste your copied path.
  2) Navigate to Editor->Inspections and expand PHP, from there, enable PHP Mess Detector validation

To use from command line:

  phpmd /path/to/file/to/inspect <format (default is xml, can also do text or html)> <arguments (most common are: codesize, unusedcode, naming)
  --- phpmd /path/to/source text codesize,unusedcode,nameing --- is the proper input format

To run from PHPStorm goto Code | Inspect Code on the main menu and follow the prompts from there

You can also create your own rule sets, see https://phpmd.org for more info.
See https://www.jetbrains.com/help/phpstorm/using-php-mess-detector.html for more info on installing and running inside PHPStorm