The Jenkins git plugin provides multiple implementations of git. Command line git is the original implementation and the reference implementation for all git plugin features. JGit is a pure Java implementation of a subset of the features of command line git using the Eclipse Foundation's JGit project. JGit provides many of the features of command line git without requiring installation of command line git.

If JGit and command line git are both enabled on an agent, the git plugin uses a "git tool chooser" to choose a preferred git implementation. The preferred git implementation depends on the size of the repository and the git plugin features requested by the job. If the repository size is less than the JGit repository size threshold and the git features of the job are all implemented in JGit, then JGit is used. If the repository size is greater than the JGit repository size threshold or the job requires git features that are not implemented in JGit, then command line git is used.

When the git tool chooser is disabled by clicking this checkbox, the git implementation specified in the job is used without considering repository size or implemented features.