Is there a way that JIRA does not show a linked issue if the user is not permitted to the other project but shows that there is a linked issue? Maybe with a warning like "The are linked issues but you are not permitted to view them".
OOB JIRA hides the link if one of the ends (issue) is not vieable (browse permissions or security level restrictions).
To achieve what you want, you would need to write a simple (really) plugin, which would display something like that using either:
- a web panel - https://developer.atlassian.com/display/JIRADEV/Web+Panel+Plugin+Module (my preferred choice)
- a calculated custom field - https://developer.atlassian.com/display/JIRADEV/Custom+Field+Plugin+Module
- tab panel - https://developer.atlassian.com/display/JIRADEV/Issue+Tab+Panel+Plugin+Module)
Cheers,
Wojtek
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