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Aside from Jira key, I want the Jira issues of my project to have unique IDs in the context of the issue type where they belong to.
Alpha Project (AP)
Beta Project (BP)
How to be able to achieve this?
Plugins? if scripting, which tools and where should I start?
Since you are new here I was wondering why issue linking is not enough for you? (Or maybe since you are new you did not know about it).
If you are unhappy with the issue linking functionlality as maybe you wanted to be able to search by links, with Scriptrunner has a lot of issuefunctions which you can use to search throught the links or sort. (But I'm sure Nic can tell you more about it since it is from Adaptavist) ;)
Have you checked out this add-on https://marketplace.atlassian.com/apps/1214561/issue-picker-custom-field-type-for-jira?hosting=server&tab=overview ? Its free and I thinks it sounds very similiar to what you need.
You will need to find or write some code to do this.
It won't be as simple as it sounds, as you'll need to think about how to store your sequence number and what happens if several processes all ask for the "next" number at the same time.
I've yet to find a public add-on to do it.
I did run into one that was owned by a large corporation and had been written in-house. As part of the engagement was to simplify their over-bloated system, we had a look at it and discovered that only the person who wrote it ever used it. Everyone else worked off the issue key.