I would recommend keeping your sources separate from the eclipse workspace, and then use the function:
Import existing project into workspace.
That way you can keep your project under source control, while leaving Eclipse manage its workspace (located elsewhere) on its own.
If you have only sources (anywhere you want), but no Eclipse project, all you need to do create a New Java project, and select your external directory as root directory for your sources.
selecting "Create project from existing sources"
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