I believe you need a bit more than just ommiting "src from the copy-dir call.
That would work if you don't use any dependencies of your own but most applications are assembled from a collection of other modules/libraries.
In that case, you want to specify the `:exclude` key in the parameter map passed to `b/uber`. It's a sequence of things to exclude where each item can also be a regex.
NOTE: If you are building your uberjar on macOS, I also suggest excluding `LICENSE` because it tends to cause issues with the case-insensitive file system.