My Jenkins instance is using GitHub App Authentication against a private GitHub Enterprise server.  I am restricted to using https (service accounts are prohibited, so no SSH or PACs).

Issue

Multibranch Pipelines are not honoring Git Tool selection, so I can't use jgit. (I have slaves where system git isn't working correctly).

Repositories Requiring Authentication

• Freestyle or Matrix Job: Git tool selection works.  I can pick jgit, and jgit is used to clone.
• Pipeline Job: tool selection is ineffective (uses git), example Jenkinsfile:

node('xxxx') {
 checkout([$class: 'GitSCM', branches: [[name: '*/main']], extensions: [], gitTool: 'jgit', userRemoteConfigs: [[credentialsId: 'ghes-app-MYORG', url: 'https://github.MYCOMPANY.com/MYORG/repo.git']]]) // uses git
}

• Multibranch Pipeline (GitHub Org Folder): tool selection is ineffective:

node("xxxx") { 
  println scm.gitTool //outputs: jgit  
  checkout scm //uses: git 
}

Output from Pipeline Job runs:

The recommended git tool is: git

Repositories Without Authentication (public repos)

Same behavior but different printout (still does not use jgit)

Example Jenkinsfile:

checkout([$class: 'GitSCM', branches: [[name: '*/master']], extensions: [], gitTool: 'jgit', userRemoteConfigs: [[url: 'https://github.com/any/any.git']]]) // uses git 

Output:

The recommended git tool is: NONE

NOTE: I do not have node-specific git tools configured anywhere in my installation.

Job Configs

(Multibranch pipeline config.xml attached)