we are trying to create an application link between JIRA and Fisheye. Both use client side certificates and both certificates are different from each other. It seems that those certificates prevent the systems for communicating with each other and creating the application link. Does anyone know how register those certificates in both systems? Does anyone have experience?
Yes, by downloading the PEM certificates and importing them into each others cacerts keystores. Depending on if you are running windows, linux or OS/X the process differs a little. Here is their documentation on the subject:
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