Cloned repository is dirty

[vshulgin]

Reproduction steps

Clone remote repository to local folder

var options = new CloneOptions
  {
    CredentialsProvider = (url, user, cred) => new UsernamePasswordCredentials { Username = userName, Password = passWord }
    };
Repository.Clone(_remoteUrl, _localPath, options);

Expected behavior

git status must return nothing to commit, working tree clean

Actual behavior

git status returns

Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
        deleted:    Managers/ashish.reddy-automation-eng.productsem-20191015.yaml
        deleted:    Managers/ashish.reddy-coaching-eng.productsem-20191003.yaml
        deleted:    Managers/ashish.reddy-coaching-eng.productsem-20191015.yaml
        deleted:    Managers/gowtham.ramachandra-coaching-Eng.Manager-20191008.yaml
        deleted:    Managers/gowtham.ramachandra-coaching-Eng.Manager-20191009.yaml
        deleted:    Managers/gowtham.ramachandra-process-improvement-Eng.Manager-20191008.yaml
        deleted:    Managers/radhesh.radhakrishnan-process-improvement-eng.manager-20191011.yaml

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
        modified:   DataStructures/automation-schema.json
        modified:   DataStructures/coaching-schema.json
        modified:   DataStructures/process-improvement-schema.json

Untracked files:
  (use "git add <file>..." to include in what will be committed)
        _git2_a18992

Version of LibGit2Sharp (release number or SHA1)

0.26.2

Operating system(s) tested; .NET runtime tested

Windows 10 Version 2004 10.0.19041
.Net Core 3.1

[ethomson]

How are you configuring your line endings? Do your line endings (as checked in to the repository) match the promises that you've made with your configuration?

A mismatch between your .gitattributes configuration (and yes, please do use .gitattributes, not core.autocrlf) and the contents in the repository are almost always to blame for this behavior.

[DaveSenn]

I've the same problem (also with version 0.26.2 on Windows 10). Cloning a new repo results in the clone repo conaining a symlinkd with name "_git2_a05268".

I tested without a .gitattributes files and `then again with the following file:

###############################################################################
# Set default behavior to automatically normalize line endings.
###############################################################################

* text=auto

*.bmp binary
*.dll binary
*.gif binary
*.jpg binary
*.png binary
*.ico binary
*.snk binary
*.exe binary
*.dll binary
*.pdb binary
*.xlsm binary
*.xlsx binary
*.xls binary
*.dox binary
*.doc binary
*.docx binary
*.pdf binary
*.obj binary
*.exp binary
*.iobj binary
*.ipdb binary
*.lib binary
*.jar binary
*.zip binary
*.pch binary
*.res binary
*.tlog binary
*.db binary
*.cache binary

*.ascx text eol=crlf
*.cd text eol=crlf
*.cmd text eol=crlf
*.coffee text eol=crlf
*.config text eol=crlf
*.cs text eol=crlf diff=csharp 
*.csproj text eol=crlf merge=union 
*.cshtml text eol=crlf
*.css text eol=crlf
*.dtd text eol=crlf
*.edmx text eol=crlf
*.htm text eol=crlf
*.html text eol=crlf
*.js text eol=crlf
*.json text eol=crlf
*.msbuild text eol=crlf
*.nuspec text eol=crlf
*.resx text eol=crlf
*.ruleset text eol=crlf
*.StyleCop text eol=crlf
*.targets text=auto
*.tt text=auto
*.txt text eol=crlf
*.vb text eol=crlf
*.vbhtml text eol=crlf
*.vbproj text eol=crlf merge=union 
*.vbs text eol=crlf
*.wsf text eol=crlf
*.xml text eol=crlf
*.xunit text eol=crlf
*.sln text eol=crlf merge=union
*.cpp text eol=crlf
*.c text eol=crlf
*.h text eol=crlf
*.mc text eol=crlf
*.def text eol=crlf
*.rc text eol=crlf
*.rc2 text eol=crlf
*.vcxproj text eol=crlf
*.manifest text eol=crlf
*.shfbproj text eol=crlf
*.rdl text eol=crlf
*.rds text eol=crlf
*.rptproj text eol=crlf

> dir

My code (.NET Core 3.1):

public static void Clone( String repoPath, String httpUrl )
{
	var credentials = GetGitCredentials();

	var cloneOptions = new CloneOptions
	{
		CredentialsProvider =
			( url, user, cred ) => new UsernamePasswordCredentials { Username = credentials.Username, Password = credentials.Password }
	};
	Repository.Clone( httpUrl, repoPath, cloneOptions );
}

[vshulgin]

There is .gitattributes file in repository

* text=auto
*.yaml text eol=lf

Files in this repository re-normalized with git add --renormalize .
Cloning with git clone results to clean repository, cloning with libgit2sharp results to dirty repository with following status:

On branch master
Your branch is up to date with 'origin/master'.

Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
        deleted:    Managers/ashish.reddy-automation-eng.productsem-20191015.yaml
        deleted:    Managers/ashish.reddy-coaching-eng.productsem-20191003.yaml
        deleted:    Managers/ashish.reddy-coaching-eng.productsem-20191015.yaml
        deleted:    Managers/gowtham.ramachandra-coaching-Eng.Manager-20191008.yaml
        deleted:    Managers/gowtham.ramachandra-coaching-Eng.Manager-20191009.yaml
        deleted:    Managers/gowtham.ramachandra-process-improvement-Eng.Manager-20191008.yaml
        deleted:    Managers/radhesh.radhakrishnan-process-improvement-eng.manager-20191011.yaml

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
        modified:   DataStructures/automation-schema.json
        modified:   DataStructures/coaching-schema.json
        modified:   DataStructures/process-improvement-schema.json

Untracked files:
  (use "git add <file>..." to include in what will be committed)
        _git2_a11820

As you may see, some files are deleted. Is it because of line-endings? I don't think so.
Also, untracked file _git2_a11820 - what is this? It is windows shortcut, pointing to un-existing directory, the name of target directory is the same as name of parent directory where the repository is cloned, i.e. repository is cloned to C:\temp\testing\eng.hub and mentioned shortcut point to C:\temp\testing\eng.hub\testing.

Any ideas?

[ethomson]

@TalyGin Ah, sorry, I see that there are deleted files now. Somebody has added files without respecting case sensitivity. Do you have a Linux user? If not, somebody has turned off core.ignorecase. They should not have. More information is available here: https://serverfault.com/a/951979/98611

[ethomson]

Regarding the _git2_a11820 junction, that was a bug during core.symlink detection. Here's the libgit2 issue: libgit2/libgit2#5147