Answer was right in front of me in the copy-dependencies mojo docs (I even linked to it). The documentation for the property includes the Expression you can refer to it by.
useRepositoryLayout: Place each
artifact in the same directory layout
as a default repository. example:
/outputDirectory/junit/junit/3.8.1/junit-3.8.1.jar* Type: boolean * Since: 2.0-alpha-2 * Required: No * Expression: ${mdep.useRepositoryLayout} * Default: false
To set this property from command line you need to run
mvn -Dmdep.useRepositoryLayout=true <goals go here>