Right now we have multiple git repositories in our Stash and each repo is a part of one module of of a bigger application which will go as a single Application when we release.
In Jira we are maintaining one Single Project and in that we have various components for each module(git repository) and each component can be released separately and can be of different version than the Full Application also different components can be part of the Full Application.
So it will be easy to maintain the life cycle of the modules which are in different repos if we can link Components to different repos.
The application linking between JIRA and Stash is on the project level and basically what you have done will cover everything. In JIRA, if you search "Project ABC and Component = XYZ", you can check that all associated issues to the result is for git repository xyz. To make this accurate, you just have to make sure that the developers are putting the correct JIRA ticket (with the right component derail) in the git commit. A hook checker might be able to pull this off.
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