We are in the process of building a new server infrastructure and will be using Appdynamics for analytics of the Java applications.
Appdynamics has a lot of features, so it seems that server metrics via collectd to Graphite will no longer be necessary. Application metrics can also be fed straight into Appdynamics.
How about Logstash, ElasticSearch and Kibana and centralised logging.
Is there still any reason to build an ELK stack for the Java developers when they can use Appdynamics?
They do different things. ELK will give you log aggregation that you can add in other functionality. Appdynamics is great for real time monitoring and profiling. I think it depends on what you're going for. Logging a distributed system and capturing error messages in one place might be very helpful with ELK. Not just that, but ELK can be used in a number of other ways. Elasticsearch can be used stand alone as a search engine or data cache.
TL;DR It depends on what you're doing. Maybe yes...maybe no...
