This similar to our setup with the slimfast-plugin. We use the maven-jar-plugin to add the Main-Class and Class-Path entries to the manifest. At build time, we use the upload goal of the slimfast-plugin to upload the dependencies. It automatically reads the configuration of the maven-jar-plugin to make sure the paths it generates match the classpath in the manifest. Then it spits out a JSON file that has info on each dependency, including its location in S3, file size, checksum, and relative path where it needs to be copied to match the Class-Path in the manifest (the JSON entries look like this https://gist.github.com/jhaber/3029dc55a568f0954b1c4b459657e...).

On deploy, the simplest way to get up and running is to use the download goal of the slimfast-plugin. It reads this JSON file, downloads each dependency (using an optional cache folder), verifies the file size and checksum, and copies it to the correct relative path. The application will then start up happily with java -jar.

At HubSpot, we instead integrated this download step more transparently into our deploy process. At build time we read this JSON file and store the dependency information in our build database. Our deploy infrastructure already accepts S3 URLs and handles downloading, caching, verifying checksums, and copying to arbitrary directories so we just piggybacked on this existing functionality to have it download the application plus all of its dependencies for us.