I develop PHP on a Mac, but I am running my code in a virtual linux machine. OS X is case-insensitive but linux is case-sensitive. Therefore PHPStorm is complaining about the mismatch with this warning message:

PHPStorm error message case-sensitivity

You will get this message every single time when you open the project which is really annoying.

To get rid of it you simply have to switch to your PHPStorm settings folder ~/Library/Preferences/WebIde100, create a file with the name idea.properties there and put in the following content:

idea.case.sensitive.fs=true

This will force PHPStorm to also work case-sensitive and prevent it from showing the message.

You need to restart PHPStorm for the setting to be used.