Ok, then the "why" is simple - that's not the way the web is intended to work, and hence Jira doesn't impose the kludge for opening in new windows or tabs because it shouldn't. Most people don't want it either, so it's never going to be done.
Trello opens the links in a new tab and it is much convenient to use in this way.
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No, it doesn't, it opens some in tabs. Some people find this convenient, most of us don't care and some despise it. (Some people actually install browser extensions that prevent the kludge from working because it's wrong)
This is not the way the web is intended to work, and Trello has implemented the kludge to do it in some places where it might make sense for some people. Jira hasn't bothered (yet) because no-one has put forward a strong enough case for doing the analysis on which links might be good to do this way and adding all the code for it in so many different places in the application.
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Because every time I want to click on a link in a user story, I would like to open it in a new window.
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Why would they?
(I mean, I know what you're thinking, but it's not clear to most from your question. I'd prefer you to explain in your own words, you will get a better answer if you do)
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