This is completely unintuitive, but in order to import an existing PHP project into IntelliJ IDEA 12.1.1, you have to create a new project into the directory with your existing sources, and choose "web module" as the type.
Do not try to import the project - it will fail to create a top level module and you'll be stuck seeing only the files in the top level of our project directory!
Source: http://stackoverflow.com/questions/13618039/intellij-php-application-losing-module-after-close
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