I just imported a project from Eclipse into Android Studio to try it out. I'm seeing some directories that have a little blue square in the lower right corner, and some directories that are blue instead of orange-ish. Does that mean something (I assume it does), and if so, what does it mean?
It means the folder is defined as an Intellij Module. Complete list of Intellij icons: https://www.jetbrains.com/idea/help/symbols.html. Follow this answer to receive notifications.
Android Studio stores the projects by default in the home folder of the user under AndroidStudioProjects. The main directory contains configuration files for Android Studio and the Gradle build files.
Blue squares: these are module roots. Equivalent of projects in Eclipse. Blue directories: these are source roots within a module.
You can explore and configure the module structure and the source directories in more detail from Project Structure (Ctrl-Shift-Alt-S).
For more information, take a look at the Project Tool Window help topic
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