Git LFS files show as deleted right after checkout

[daniel88ferreira]

Jenkins and plugins versions report

Environment

Jenkins: 2.541.3
OS: Linux - 4.18.0-553.109.1.el8_10.x86_64
Java: 21.0.9 - Eclipse Adoptium (OpenJDK 64-Bit Server VM)
---
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In a regular multibranch job fetching from BitBucket server, there are repositories (not all) that become dirty right after checkout (with GIT LFS pull enabled).

So, we execute: git status --porcelain we get
10:46:58 D Path/to/File/onGITLFS.png

The agent is a windows 2019 container with this installed:

• git version 2.51.2.windows.1
• git-lfs/3.7.1 (GitHub; windows amd64; go 1.25.1; git b84b3384)

The reason that leads me to open this bug report is that if I explicitly execute git lfs pull, the checkout is then correct. Which makes me suspect there is an issue in the way the plugin in checking out the the LFS objects.

Also, using git LFS 3.6.1 the checkout works correctly.

What Operating System are you using (both controller, and any agents involved in the problem)?

Controller is a Linux docker image
Agent is a Windows 2019 container

Reproduction steps

1. Configure a multi branch pipeline job that fetches a repository with GIT LFS enabled
2. Trigger the build.
3. Run, as the first step: bat "git status --porcelain"

Expected Results

Command outputs nothing, meaning that repository is clean after checkout

Actual Results

Command output shows dirty repository, similar to: D Path/to/File/onGITLFS.png

Anything else?

No response

Are you interested in contributing a fix?

No response

[MarkEWaite]

I can't duplicate the issue that you're reporting. I tested with the following Pipeline:

pipeline {
    agent {
        label 'windows'
    }

    stages {
        stage('Checkout') {
            steps {
                checkout scmGit(branches: [[name: 'lts-with-plugins']],
                         extensions: [cloneOption(depth: 1, honorRefspec: true, noTags: true, shallow: true),
                                      localBranch(),
                                      lfs()
                                     ],
                         gitTool: 'Default',
                         userRemoteConfigs: [[refspec: '+refs/heads/lts-with-plugins:refs/remotes/origin/lts-with-plugins',
                                              url: 'https://github.com/MarkEWaite/docker-lfs.git']])
                bat 'git status'
            }
        }
    }
}

The results were:

05:23:57  C:\J\VG\workspace\Docker\Docker-LFS\git-3951-windows-git-lfs>git status 
05:23:57  On branch lts-with-plugins
05:23:57  nothing to commit, working tree clean

I'm running Git 2.53.0.3 with git LFS 3.7.1

Are you using the lfs() extension in your Pipeline definition?

[daniel88ferreira]

Hello @MarkEWaite ,
Thanks for the quick response!

We use the bitbucket branch source plugin and we have enabled "Git LFS pull after checkout" option.

What's hard on this issue is that I can only reproduce this in some repositories -- if I create a new repo with LFS, all works correctly.
Maybe this has something to with the history of those specific repos? Also, these repos have quite some lfs files.

I can try to checkout the code the same way as you did, see if the issue happens and then get back to you.

Also, is there something else I can do to help with the debug?

[MarkEWaite]

Also, is there something else I can do to help with the debug?

Identify the differences between the passing case and the failing case. Since it is intermittent in your environment, I am unlikely to duplicate it in my environment. I only have the free plan for bitbucket.org and that limits me to not more than 1 GB of large file storage.