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HOWTO: Use WSL and its Git in a mixed development environment

How to setup a development environment where Git from WSL integrates with native Windows applications, using the Windows home folder as the WSL home and using Git from WSL for all tools.

Note if using Git for Windows, or any tool on the Windows side that does not use Git from WSL then there will likely be problems with file permissions if using those files from inside WSL.


These are the tools I use:

  • git (wsl) - Command line git from within WSL.
  • Fork (windows) - Git GUI (must be used with wslgit)
  • wslgit - Makes git from WSL available for Windows applications. Important! Follow the installation instructions and do (at least) the first optional step and then the Usage in Fork instructions.
  • KDiff3 (windows) - Diff/merge GUI tool, invoked from git inside wsl.
  • VSCode (windows)
  • A terminal, like wsltty or Windows Terminal (windows)

WSL Installation

  1. First time? Open PowerShell and run:

    Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux
  2. Download and install a distro from Windows Store, Command-Line or manually unpack and install (for Windows Server).

Important! Start WSL once directly after installing the distribution of choise to finish the installation.

For full details see

User Name and Password

When selecting a WSL user name you don't need to use the same name as your windows logon. The password can be anything but you must remember it since it will be used when sudo-ing.

The user name and password in WSL have nothing to do with the Windows user name and password, so changing your password in windows does not change your password in WSL, or vice versa.
The password you use in WSL is not critical for security since you still need to log on to your windows account to start WSL so it can be an easy to remember password. And you could simply just log on to the wsl instance as root using wsl -u root...
However, if you enable access to your WSL via SSH and allow password authentication then your WSL password strength will be of importance. But don't allow password authentication, just use pubkey authentication.

WSL Setup


In WSL, create (or edit) the file /etc/wsl.conf:

enabled = true
root = /
options = "metadata,umask=022,fmask=111,case=off"

Restart all active WSL sessions, can be done from cmd or PS using the command wsl --shutdown.

root = / changes the mount root for windows local drives to '/' instead of the default '/mnt/, so instead of C: mounted at '/mnt/c' it will be mounted at '/c'.

case=off will make all directories created from within WSL to be case insensitive in the windows file system, because even if Windows is case sensitive the applications run on windows is not necessary case sensitive.

metadata, umask and fmask

The metadata option will make it possible to set the owner and group of files using chown and modify read/write/execute permissions in WSL using chmod. See Chmod/Chown WSL Improvements for details.

The umask and fmask sets the default values of the permissions on files and directories of mounted windows drives. The umask=022 option excludes write permission for group/others for files and directories, and the fmask=111 option excludes execution permission for user/group/others for files, making the default mask 644 on all windows drives mounted automatically by WSL. The permissions can be changed by using chmod, which will create metadata for a file containing the modified permissions.

Important! This will make ALL files and directories in /c have 644 as default permissions, meaning that it won't be possible to execute any applications or scripts in the windows drives unless you specifically add the execute permission from within WSL

This is what makes permissions work as expected for the Windows filesystem from within WSL instead of every file having the execution bit set, which is really annoying, but there are some caveats.

  1. To run a Windows application (.exe) you must chmod +x the application.
  2. To chmod files in C:\Program Files or C:\Program Files (x86) the WSL terminal must be started using "Run as administrator". It doesn't seem to be possible to change permissions on files in C:\Windows anymore.

Program Xyz.exe is not working anymore!

Add the execution permission for the application:

chmod +x /path/to/xyz.exe

Note that all files in '/c/Windows/', '/c/Program Files/' and '/c/Program Files (x86)/' requires the WSL terminal to be started as administrator to be able to modify the permissions.

It seems like it is not possible anymore to change permissions of files in '/c/Windows/'.

Scripts does not work after git checkout!

When doing git-checkout from a windows tool and a script file is replaced then it might will loose its metadata, which means loosing the execution permission. If trying to execute the script you will get a Permission denied, and if doing a git diff you will just get a difference in mode:

$ git diff
diff --git a/myscript b/myscript
old mode 100755
new mode 100644

Just restore the missing execution permission using chmod +x myscript for that file in WSL.

You can also do a git checkout -- myfile from within WSL, to restore the permissions for that file by checking it out again, but note that this will also revert any other changes made to that file. git checkout -- . can be useful to restore the permissions on several files in the current directory and all subdirectories, but be aware that this command will revert ALL changes made to all files.

Use Windows Home Folder

Run the following command from PS or cmd, make sure that the path to the Windows user folder and the wsl username are correct:

wsl -u root usermod --home /c/Users/win-user wsl-user 

Close all WSL sessions (wsl --shutdown from cmd/PS) before restarting again.

Existing Files/Folders Permissions

If you already have ssh keys and configurations in $HOME/.ssh that were created in windows then you must change the file permission on those files to 600. Also fix $HOME/.gnupg if you are using GnuPG.

chmod -R 600 .ssh
chmod -R 600 .gnupg

Share Environment Variables from Windows to WSL

Windows environment variables are shared to WSL using a special environment variable called WSLENV that is a colon-delimited list of environment variables. WSLENV can also be used to share environment variables from WSL to Windows, useful when executing windows applications from WSL.

Each variable can be suffixed with a slash followed by flags to specify how it is translated, for example /up makes the variable available when invoking WSL from Win (p flag) with the path translated to WSL paths (u flag).

(Optional) /tmp in RAM

$ echo "tmpfs /tmp tmpfs rw,noatime,nosuid,nodev,size=1G" | sudo tee -a /etc/fstab

The above command will add an entry in fstab that will mount a temporary filesystem on /tmp which will use a maximum of 1 GB of RAM. Omitting size will use the default max which is half(?) the RAM.

GIT Setup

wslgit - the bridge between Windows and git in WSL

Download wslgit (follow the installation instructions!).

Speed up wslgit

By default wslgit executes most commands using non-interactive shell which does not execute .bashrc etc and therefore is fast.
But commands that access remotes (clone, fetch, push, pull, etc.) are executed using interactive shell which do run .bashrc. If the .bashrc script contains a lot of initializations, like starting agents and other time consuming stuff then those commands can become slow.

The environment variable WSLGIT can be used to detect that .bashrc was started by wslgit, and if so only do a bare minimum of initialization, just so git can work properly, like starting ssh-agent etc.
If running .bashrc is not required then wslgit can be forced to always use non-interactive shell by, in Windows, define an environment variable named WSLGIT_USE_INTERACTIVE_SHELL and set it to false.

Using KDiff3 for diff and merge

  1. Add KDiff3 installation directory to the windows path so that WSL can find kdiff3.exe without the full path, makes the configuration prettier.
  2. Create a difftool config in .gitconfig for KDiff3, call it "kdiff3", whose command converts paths from unix-style to windows style, and configure it as diff.tool. Also configure KDiff3 as mergetool, which does not require any conversion of paths.
        guitool = kdiff3
        prompt = false
    [difftool "kdiff3"]
        # Unix style paths must be converted to windows path style
        cmd = kdiff3.exe \"`wslpath -w $LOCAL`\" \"`wslpath -w $REMOTE`\"
        trustExitCode = false
        tool = kdiff3
        keepBackup = false
        prompt = false
        path = kdiff3.exe
        trustExitCode = false

VSCode Setup

Using git from WSL in VSCode

By using the VSCode plugin Remote - WSL and open a folder "in WSL" then VSCode will always use git from WSL, but for folders not opened using the Remote WSL then wslgitmust be in the Windows Path, which it is if you did the optional second step when installing wslgit.

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The kdiff3 integration is even easier when using wslpath, and there is no need to share TMP since the windows side now has access to the entire WSL filesystem via \wsl$.

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Moved wslgit instructions from VSCode section to first in Git Setup

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I only managed to get kdiff3 to work as a mergetool by using this line:

cmd = '/mnt/c/Program Files/KDiff3/kdiff3.exe' \"`wslpath -w $BASE`\" \"`wslpath -w $LOCAL`\" \"`wslpath -w $REMOTE`\" --output \"`wslpath -w $MERGED`\"

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I only managed to get kdiff3 to work as a mergetool by using this line:

cmd = '/mnt/c/Program Files/KDiff3/kdiff3.exe' \"`wslpath -w $BASE`\" \"`wslpath -w $LOCAL`\" \"`wslpath -w $REMOTE`\" --output \"`wslpath -w $MERGED`\"

I did some testing and for WSL2 it appears that the custom difftool.kdiff3.cmd is not needed anymore 👍 .
For WSL1 I still have to use the custom difftool.kdiff3.cmd but I don't need a custom mergetool.kdiff3.cmd.

Which WSL version are you using?
And what version of KDiff3? I'm using the really old kdiff3 Version 0.9.98 (64 bit). There is a newer version maintained by KDE which is not working at all for me.

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Argh, I just noticed last night that git will copy files to /tmp sometimes when I run git difftool, and my kdiff3 doesn't recognize UNC at all!
Version for my kdiff3 is 1.8.4, 64 bit. I run WSL2 too.
Think I'll give meld a try :<

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Meld works much better than kdiff3, just slow launch and somehow sluggish compared to kdiff3 but at least UNC is fundamental in WSL2 development :/

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Ridder90 commented Jan 22, 2021

After applying the meta I cannot start docker-compose.exe and explorer.exe anymore because of the permission denied. Unfortunatly i cannot add the execution permission.

sudo chmod 775 '/mnt/c/Program Files/Docker/Docker/resources/bin/docker-credential-desktop.exe'
[sudo] password for florian:
chmod: changing permissions of '/mnt/c/Program Files/Docker/Docker/resources/bin/docker-credential-desktop.exe': Permission denied

Even while i am the owner of those files :S Any ideas?

EDIT: actually it seem to work by also adding the root=/ . Not sure why though 🤔

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Even while i am the owner of those files :S Any ideas?

You must start the WSL2 terminal as administrator (Run as administrator) to be allowed to chmod files in Windows or any of the two Program Files folders. No need for sudo then since it is a Windows permission issue and not on the Linux side.

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Thanks for your help! I opened wsl with Run as administrator, but unfortunately still cannot change the permissions.

florian@T490-WIN:/c/WINDOWS/system32$ chmod +x cmd.exe                                                                                                  
chmod: changing permissions of 'cmd.exe': Permission denied                                                                                             
florian@T490-WIN:/c/WINDOWS/system32$ sudo chmod +x cmd.exe                                                                                             
[sudo] password for florian:                                                                                                                            
chmod: changing permissions of 'cmd.exe': Permission denied         

I will do my own research. But any help is very much appreciated :)

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@Ridder90 It appears that I actually cannot change permissions on anything in C:\Windows, but C:\Program Files works, for example docker-credential-desktop.exe.
The strange thing is that I must have been successful at some time because C:\Windows\write.exe has execute permissions.

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Carl why do you need to do this instead of invoking git.exe offered in Windows git release instead?

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@HankAviator Windows git doesn't honor the mode bits for a file, which cause problems if checking out with windows-git and then work on the files in WSL.

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After running this step:

in WSL, edit /etc/passwd and change your home folder:

I am unable to use wsl anymore, because it seems wsl doesn't have rights:

PS C:\Users\Aleksandr> wsl
-bash: /etc/profile: Permission denied
-bash-4.4$ cd /
-bash-4.4$ cd etc
-bash: cd: etc: Permission denied

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I am unable to use wsl anymore, because it seems wsl doesn't have rights:

Hi, I assume you have found a solution to your problem by now :)
If not, some things you could do is first run wsl as the root user using wsl -u root and check that the passwd file is correct. You could use the command lslogins -l -o UID,USER,HOMEDIR,SHELL to verify the information, verify the homedir path. (I've updated the instructions with a safer way to modify the home directory)

If you manage to solve the problem or find its root cause it would be really nice if you could share it :)

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vscode with Remote - WSL is so slow for me, also it opens files in a new vscode instance. I had to write a function to make it work the way i wanted

function code {
		for in_file in $@; do
			code_infile+=$(wslpath -w $in_file)
			code_infile+=' '
		"/mnt/c/Program Files/Microsoft VS Code/bin/code" $code_infile

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Hey Carl, on my fork I wrote about how to configure git for windows to work with WSL. If the repos are in Windows file system, it'll boost the performance. However I do believe I should add the mode bits concern in it.

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