I have few user installed plugins such as hipchat, mobile plugin etc... How can I migrate these user installed plugins from jira server to jira cloud using jira migration assistant.
You do not.
Jira Server and Jira Cloud are two totally different pieces of software. They share a name, a function, an owner and some code and look-and-feel, but they're different systems.
The app (plugin) architecture for both is totally different. A Cloud app cannot be installed on Server, and a Server app can not be installed on Cloud (by users).
Like the services, a lot of apps in the marketplace have equivalents - the obvious example for me is Scriptrunner for Jira. I can tell you that SR for Cloud is not just a modification of the SR for Server, our product team wrote a new thing from scratch, using totally different technology.
For each app you have installed, you are going to need to look for a migration path. JMCA is gradually having conversion code added to it to handle some of the bigger apps, and try to handle some of the easier generic conversions from Server to Cloud, but for most apps, it's not going to do all of it.
You are going to need to look at every app you have, analyse how you're using it and what it does, and work out a migration path for yourself. Sometimes, JMCA will cover it. On the most part, it will not.
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