I've noticed that the Tool Location configuration I've setup gets removed whenever anyone returns to edit the system configuration.

• Manage Jenkins -> Configure System
• Create a vSphere Cloud and Template
• In the template configuratnoi, check "Tool Locations" -> and provide a tool and path. In my case I'm overriding a git configuration I created with the Git client plugin in the Global Tool Configuration section called "git-default". I've noticed the effect occurs with other tools and it doesn't matter if you have multiple tools set here.
• Provide the path to the tool and save. The override I'm doing will show up in the generated templates after the agent is created and the jobs will pick up the tool override.
• Return to the "Configure System" page, scroll down and notice that the Tool Configuration information is no longer present. If you save at this point, the tool override value is lost.

The big ugly hassle is we have a lot of systems now using templates and jobs that utilize them work well until someone edits and saves the Jenkins configuration page. Because we're using it to setup the git path for jobs on the generated agent, all the jobs using the templates start failing until we go back an re-setup the tool configuration. Developers complain and hate on Jenkins, we look silly, etc. . There's no way we're going to always remember to reconfigure all the tools to their specific needs every time someone admins Jenkins here.