The typical system administrator, to urgently recover from a problem, will need to use local system commands to disable plugins indicated a problem in the Jenkins logs.
The first step is to include a "README" in the install and/or plugin directories. This readme file may be as simple as to link to the Jenkins online documentation describing the file structure and configurations.
Secondly, there should be clear documentation on the "manual" backup/restore/disabling plugins and their configurations.
Lastly, if it is not currently possible to disable a plugin via the command line and/or config update a process should be added to Jenkins to do so.