Gradle: What is the difference between classpath and compile dependencies?

I'm going to guess that you're referencing compile and classpath within the dependencies {} block. If that is so, those are dependency Configurations.

A configuration is simply a named set of dependencies.

The compile configuration is created by the Java plugin. The classpath configuration is commonly seen in the buildSrc {} block where one needs to declare dependencies for the build.gradle, itself (for plugins, perhaps).

If buildscript itself needs something to run, use classpath.

If your project needs something to run, use compile.

The buildscript{} block is for the build.gradle itself.

For multi-project building, the top-level build file is for the root project, the specific build file is for sub-project (module).

Top-level build file where you can add configuration options common to all sub-projects/modules.

Do not place your application dependencies in top-level build file, they belong in the individual module build.gradle files