Then the classpath is determined by your runtime configuration, which in turn is influenced by how your project is configured. For example, if you have multiple source directories, they'll all get compiled to the configured output directory (there are several ways to configure output directories).
As long as the file is on the classpath it doesn't matter where it is. For example, a Maven application would put config files in src/main/resource. So you could create another source directory and put it there. Putting it at the root level of your project itself, in my opinion, is a bad idea.
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