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Enable the plugin with

addSbtPlugin("io.get-coursier" % "sbt-shading" % "2.1.1")

in project/plugins.sbt. sbt-shading requires sbt >= 1.3.0.

Then use settings like the following:

// Enable the plugin

// Add the dependencies to shade along the other (non-shaded) ones
libraryDependencies += "io.argonaut" %% "argonaut" % "6.2"
libraryDependencies += "org.scalameta" %%% "trees" % "4.8.5"

// Tell the plugin to shade some dependencies.
// This also shades all their transitive dependencies, except those
// that are also brought by non-shaded dependencies.
// This merges those dependencies JARs in our output JAR, along with our
// classes.
// NB: the version itself doesn't matter but `%%` vs `%%%` does
shadedDependencies += "io.argonaut" %% "argonaut" % "<ignored>"
shadedDependencies += "org.scalameta" %%% "trees" % "<ignored>"

// Tell the plugin to rename some namespaces in the output JAR.
// This renames any of our classes in this namespace, and adjusts
// any reference in this namespace.
// Be sure that all classes in this namespace are effectively
// in the output JAR.
shadingRules += ShadingRule.moveUnder("argonaut", "test.shaded")

// Tell the plugin that the output JAR can contain classes in that
// namespace. Fail loudly if it finds any class outside of it.
validNamespaces += "test"