NetBeans has become my IDE of choice for PHP in the last year or so. Version 7.4 shipped with support for code analysis tools with PHP, namely PHPMD and PHP_CodeSniffer. Unfortunately, usage of these tools within the IDE is not well documented, so I wanted to share how they work.
Installing the tools is up to you; NetBeans just uses the scripts you point to. I prefer using composer's global option, but if you prefer PEAR or some other installation method, that's fine too.
Once installed, navigate to "Tools > Options > PHP > Code Analysis" inside of NetBeans and configure the paths to the scripts and the default rules you want to use.
Now here's the part nobody really tells you: how to actually use these tools. From inside of NetBeans, navigate to "Source > Inspect..."
That's pretty much it. Select the scope and and configuration to use and click "Inspect." If you configured everything correctly, the scripts will run and after a few seconds (or minutes, depending on project size) you'll be presented with a nice results view.
You may want to instruct the IDE to ignore certain folders when running code analysis. For example, I use Composer to manage dependencies, and I don't want to see results for everything under my vendor directory. To ignore vendors, right-click on the project in the project pane and navigate to "Properties > Ignored Folders" and add the vendors folder under "Extra Folders for Code Analysis."