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what color would you like to change namely?

The black Project tool window background is defined in UI theme. UI themes (used for dialogs, tool windows, etc.) are Java Look&Feels. This is a standard way to style Swing applications. As such, they are hardcoded and can't be changed easily.

Note that it's technically possible to install any third-party L&F into JVM and use it in WebStorm ( see http://docs.oracle.com/javase/tutorial/uiswing/index.html, https://weblogs.java.net/blog/kirillcool/archive/2005/08/intellij_idea_5.html for instructions). Custom themes can also be implemented as plugins, like Material UI and Afterglow Theme - you can give them a try.

We’re working on a feature allowing themes customization in IntelliJ Platform. Please follow IDEA-132299 to get updates

Green and yellow colors used for test files and library files are scope colors that can configured in Settings | Appearance & Behavior | File Colors

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