This problem may be caused by a custom (a self-signed) certificate. Make sure to install the latest JRE and then change the JAVA_HOME of Jira server.
The above solution should work, otherwise, see below for the steps to workaround this issue:
From your Jira Server, clone the repository manually using the git client.
git clone --mirror https://my-self-signed-repo/project.git
Make sure that the Jira user has access to the folder above.
Configure the repository to disable verification of the SSL certificate.
git config http.sslVerify false
Run git config http.sslVerify false in the repository folder.
From your browser, log into Jira and add a repository via Administration>Add-ons/Applications(Jira 7).
Select Git Repositores under Git Integration for Jira.
Click Connect to Git Repository then Advanced setup.
For the Display Name, enter a description of the Git repository.
For the Repository Root, enter the full path to the Git repository that you have cloned. Considering the example in step 1, it will be similar to /jira/home/data/git-plugin/project.git.
Click the Detect button next to the Repository Origin.
Click Add to add this repository to the Git repository configuration list.
The clone will be kept up-to-date and the SSL verification issues will be ignored.
There are alternative solutions to make Java trust this certificate. Please refer to the following articles from Atlassian which focuses on helping to resolve SSL Verification Issues:
If the problem persist, please send us a support zip to give us a better view of the issue.
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