I have a Jira Connect App already hosted in Atlassian Marketplace. I am aware of the marketplace requiring server version for Jira On-Prem, But I searched everywhere I couldn't find any documentation of how do we host our app(same app as cloud) as a On-Prem Application. And if so Do we require two different apps, in this case how do we maintain it? And How do we use REST API's to query Jira Data like fetching issue meta data etc?
The short version is "start again".
Cloud and Server/DC have fundamentally different app frameworks, and an app for one simply has no way of working on the other.
You can probably re-use a lot of logic (and if your connect app is written in a java-like language, possibly code for some the logic as well), but you'll need a completely different framework/structure for the app.
It seems like you do not even have basic knowledge about creating apps, but this site can help you with that:
https://developer.atlassian.com/developer-guide/cloud-development-platform-overview/
If you want to query data from Cloud, you have Rest API site, with every needed info:
https://developer.atlassian.com/cloud/jira/platform/rest/v3/
There are many tutorial for beginners regarding "how to use REST API" topic.
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