If you are interested in debugging the web service layer or other parts of the app that are written in Clojure, there are lots of options available. The Clojure REPL is often the most useful tool, as it makes it very easy to interact with individual functions and namespaces.

If you are looking for more traditional debugging capabilities, such as defining breakpoints and stepping through the lines of your source code, there are many options. Just about any Java debugging tool will work to some degree, but Clojure-specific tools such as CDT and debug-repl will have better integration with your Clojure source files.

For a more full-featured IDE, Cursive is a great option. It's built on IntelliJ IDEA, and provides a debug REPL that supports all of the same debugging features that are available in Java; breakpoints, evaluating expressions in the local scope when stopped at a breakpoint, visual navigation of the call stack across threads, etc.

Debugging the Ruby code running in Puppet Server can be a bit trickier, because Java and Clojure debugging tools will only take you into the JRuby interpreter source code, not into the Ruby code that it is processing. So, if you wish to debug the Ruby code directly, you'll need to install gems and take advantage of their capabilities (not unlike how you would debug Ruby code in the MRI interpreter).

For more info on installing gems for Puppet Server, see Puppet Server and Gems.

Please note that a REPL running in Ruby is incompatible with lein repl because JRuby will not receive data from standard input when running inside of lein repl. To use a ruby REPL during development run puppetserver from source with lein run rather than lein repl:

$ lein run --config ~/.puppetserver/puppetserver.conf

The lein run command will start the server in the foreground as normal. pry or ruby-debug will display an input prompt when the relevant statement is reached. Expect to see the normal lein run output and then the Ruby REPL will present itself as compared to lein repl which presents a prompt early in the process lifecycle. In this way the "ruby repl" is more of a breakpoint than a REPL in the Clojure sense.

We are aware that some favorite gems/tools/features for ruby debugging don't currently work with JRuby/Puppet Server. (For example, some things like color syntax highlighting in Pry.) It's important to us to make sure that the Ruby developer experience is not degraded for developers working via Puppet Server rather than webrick, so, if you run into issues like this, please file an issue on our Bug Tracker, and we will see if it's possible to add support for things that we're missing. In many cases it might be a matter of simply submitting a patch to JRuby, or submitting a JRuby-compatibility patch for an existing gem, and we're interested in trying to help with those sorts of things whenever possible.