Directory Structure

This matches a typical IDE directory structure. For Maven users the source root is "src/main/java" and assets are placed in "src/main/resources". This allows easy packaging and deployment, as all assets packaged into jar will continue loading with exactly the same code.

IntelliJ IDEA (with Maven / Gradle)

Structure (Uber jar)

project directory (typically project name)
    src (source code directory)
        assets
            textures (image files ".png", ".jpg")
            sounds (sound files ".wav")
            music (music files ".mp3")
            json (JSON files / levels ".json")
            tmx (TMX levels ".tmx")
            text (text files ".txt")
            data (binary data files with custom extensions)
            ui/css (stylesheets for customizing UI elements)
            ui/fonts (fonts ".ttf", ".otf")
        (your packages / code)