Jenkins provides both - Web based UI and API(s).Hence, we can automate Jenkins. In case of integration between Remedy and Jenkins, AE will sit in between those two and get job done on Jenkins based on ticket or request in Remedy.
As about deployment of multiple Java application, do provide more details on what will be using to deploy these applications. If they are again using Jenkins for the same, we can automate that. If they are using some other tool or software, we will need to check the feasibility. That being said, on a very high level, as long as the tool provides some way to interact with it, we should be able to automate it.