I am observing this issue as well. My error log looks the same as the one posted above. I was not attempting to make a Github update. My Github configuration was setup long ago and is still working today. I was attempting to set up the E-mail Notification option. I was able to send a test email (Test configuration by sending a test e-mail) so the configuration I added appeared to be correct. When I selected the Save button the exception was displayed. When I re-entered the configuration page I noticed my E-mail Notification settings were not saved. I then tried setting up the Global Slack Notifier Settings and then selected the save button and the exception was displayed again. I received a message in my Slack channel (added an integration to this channel: jenkins) so I believe I configured it correctly. If I go into the Configure System menu and then press the save button the exception will be displayed, even with NO changes being made. I would appreciate any advice on this issue. Thank you for all your help!
I was able to get around this Malformed GitHub exception by setting up my GitHub Server in the "Configure System" page. Previously I only had to configure GitHub in the "Source Code Management" section of my Maven project. I am just happy its business as usual again!