Elasticsearch, prior to version 2.0, was packaged as a JAR with some dependencies shaded to prevent version conflicts for Java users embedding it in their applications, but this approach created complexity and debugging challenges. From version 2.0 onwards, Elasticsearch opted to eliminate shading, requiring developers to manage dependencies like Joda and Guava manually to avoid conflicts. The text provides a detailed guide on how to handle these conflicts through dependency relocation and shading within a Maven project, offering an example of how to use the Elasticsearch transport client with different versions of Joda. The document also hints at future plans to reduce dependency conflicts by replacing some third-party libraries with native Java alternatives and potentially developing a lightweight Java client for Elasticsearch. Despite the challenges of implementing these changes, the aim is to simplify dependency management and improve the overall development experience.