Editing Troubleshooting of GIT (section)

=== SSH Authentication Failed: Permission denied (publickey) ===

'''Error Message'''

After running the command:

<pre>
git clone git@github.com:your-org/your-repo.git /opt/your-app
</pre>

you may see the following error:

<pre>
Cloning into '/opt/your-app'...
git@github.com: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights and the repository exists.
</pre>

A similar error may also occur when running:

<pre>
git pull
</pre>

or:

<pre>
sudo git pull
</pre>

'''Cause'''

This error occurs when Git cannot authenticate with GitHub over SSH.

Common causes include:

* The SSH key does not exist on the server.
* The SSH key has not been added to GitHub.
* The SSH key is added to the wrong GitHub account or the wrong repository.
* The repository is private and the key does not have access.
* The server has multiple SSH keys, but Git is using the wrong one.
* The key is a GitHub Deploy Key that belongs to another repository.
* `sudo git clone` or `sudo git pull` is being used, causing Git to use the `root` user's SSH key instead of the deploy user's SSH key.

For example, if you run:

<pre>
ssh -T git@github.com
</pre>

and see:

<pre>
Hi other-org/other-repo! You've successfully authenticated, but GitHub does not provide shell access.
</pre>

it means the current SSH key is valid, but it is linked to another repository's Deploy Key. In that case, GitHub may return:

<pre>
ERROR: Repository not found.
</pre>

even if the target repository URL is correct.

'''Recommended Solution — Use a dedicated SSH alias for the project'''

This is the safest approach when the server has multiple GitHub Deploy Keys.

Assume:

<pre>
Deploy user: your-user
App path: /opt/your-app
Private key: /home/your-user/.ssh/id_ed25519_your_app
Public key: /home/your-user/.ssh/id_ed25519_your_app.pub
Repository: git@github.com:your-org/your-repo.git
</pre>

'''Step 1 — Check the key exists'''

<pre>
ls -l ~/.ssh/id_ed25519_your_app*
</pre>

Expected result:

<pre>
/home/your-user/.ssh/id_ed25519_your_app
/home/your-user/.ssh/id_ed25519_your_app.pub
</pre>

If the key does not exist, create one:

<pre>
ssh-keygen -t ed25519 -C "your-app-deploy-key" -f ~/.ssh/id_ed25519_your_app
</pre>

'''Step 2 — Add the public key to GitHub'''

Print the public key:

<pre>
cat ~/.ssh/id_ed25519_your_app.pub
</pre>

Add it to the target repository:

<pre>
GitHub Repository
→ Settings
→ Deploy keys
→ Add deploy key
</pre>

If the server only needs to clone or pull the repository, do not enable write access.

'''Step 3 — Configure SSH alias'''

Edit the SSH config file:

<pre>
nano ~/.ssh/config
</pre>

Add:

<pre>
Host github-your-app
  HostName github.com
  User git
  IdentityFile ~/.ssh/id_ed25519_your_app
  IdentitiesOnly yes
</pre>

Fix SSH file permissions:

<pre>
chmod 700 ~/.ssh
chmod 600 ~/.ssh/config ~/.ssh/id_ed25519_your_app
chmod 644 ~/.ssh/id_ed25519_your_app.pub
</pre>

Explanation:

# <code>~/.ssh</code> should be accessible only by the current user 
# <code>~/.ssh/config/</code> should be readable/writable only by the current user 
# <code>~/.ssh/id_ed25519_your_app</code> private key should be readable only by the current user 
# <code>~/.ssh/id_ed25519_your_app.pub</code> public key can be readable by others

'''Step 4 — Test the SSH alias'''

Run:

<pre>
ssh -T github-your-app
</pre>

Expected result:

<pre>
Hi your-org/your-repo! You've successfully authenticated, but GitHub does not provide shell access.
</pre>

The message:

<pre>
GitHub does not provide shell access.
</pre>

is expected. It means SSH authentication works, but GitHub does not allow interactive shell login.

If the result shows another repository, for example:

<pre>
Hi other-org/other-repo! You've successfully authenticated, but GitHub does not provide shell access.
</pre>

then the alias is not using the intended key, or the key was added to the wrong repository.

'''Step 5 — Clone using the SSH alias'''

Instead of:

<pre>
git clone git@github.com:your-org/your-repo.git /opt/your-app
</pre>

use:

<pre>
git clone git@github-your-app:your-org/your-repo.git /opt/your-app
</pre>

If `/opt/your-app` requires root permission to create, prefer creating the directory first and assigning ownership to the deploy user:

<pre>
sudo mkdir -p /opt/your-app
sudo chown -R your-user:your-user /opt/your-app
git clone git@github-your-app:your-org/your-repo.git /opt/your-app
</pre>

This avoids using `sudo git clone`.

'''Step 6 — If the repository already exists, update the remote URL'''

Check the current remote:

<pre>
cd /opt/your-app
git remote -v
</pre>

If it uses the default GitHub host:

<pre>
origin  git@github.com:your-org/your-repo.git (fetch)
origin  git@github.com:your-org/your-repo.git (push)
</pre>

change it to use the SSH alias:

<pre>
git remote set-url origin git@github-your-app:your-org/your-repo.git
</pre>

Verify:

<pre>
git remote -v
</pre>

Expected result:

<pre>
origin  git@github-your-app:your-org/your-repo.git (fetch)
origin  git@github-your-app:your-org/your-repo.git (push)
</pre>

Then run:

<pre>
git pull
</pre>

'''Avoid using sudo with Git'''

Avoid:

<pre>
sudo git clone git@github.com:your-org/your-repo.git /opt/your-app
sudo git pull
</pre>

Because `sudo` runs Git as `root`, Git may use root's SSH keys instead of the deploy user's SSH keys.

If the app directory is owned by `root`, fix ownership instead:

<pre>
sudo chown -R your-user:your-user /opt/your-app
</pre>

Then run Git commands as the deploy user:

<pre>
cd /opt/your-app
git pull
</pre>

'''Related Issue: dubious ownership'''

If Git shows:

<pre>
fatal: detected dubious ownership in repository at '/opt/your-app'
</pre>

it means the current user and the repository owner do not match.

Check:

<pre>
ls -ld /opt/your-app
whoami
</pre>

If the app should be maintained by the deploy user, fix ownership:

<pre>
sudo chown -R your-user:your-user /opt/your-app
</pre>

Alternatively, mark the directory as safe:

<pre>
git config --global --add safe.directory /opt/your-app
</pre>

For deployment directories, fixing ownership is usually cleaner if the deploy user is expected to run `git pull`.

'''Alternative Solution — Pass the SSH key inline'''

You can also override the SSH command directly.

First, test the key:

<pre>
ssh -T -i /path/to/.ssh/your_key_name -o IdentitiesOnly=yes git@github.com
</pre>

Expected result:

<pre>
Hi your-org/your-repo! You've successfully authenticated, but GitHub does not provide shell access.
</pre>

Then clone:

<pre>
GIT_SSH_COMMAND='ssh -i /path/to/.ssh/your_key_name -o IdentitiesOnly=yes' \
  git clone git@github.com:your-org/your-repo.git /opt/your-app
</pre>

If you need to run this with `sudo`, preserve the environment explicitly:

<pre>
sudo GIT_SSH_COMMAND='ssh -i /path/to/.ssh/your_key_name -o IdentitiesOnly=yes' \
  git clone git@github.com:your-org/your-repo.git /opt/your-app
</pre>

However, this is usually less clean than using an SSH alias, especially for long-term maintenance.

'''Notice'''

<pre>
-o IdentitiesOnly=yes
</pre>

forces SSH to use only the specified key and prevents SSH from trying other keys loaded in the agent. This is important on servers with multiple Deploy Keys.

'''Summary'''

Recommended long-term setup:

<pre>
# 1. Create or confirm a dedicated deploy key
ls ~/.ssh/id_ed25519_your_app*

# 2. Add the public key to the target GitHub repository Deploy Keys
cat ~/.ssh/id_ed25519_your_app.pub

# 3. Configure SSH alias
nano ~/.ssh/config

# 4. Test alias
ssh -T github-your-app

# 5. Clone or update remote using alias
git clone git@github-your-app:your-org/your-repo.git /opt/your-app

# or, for an existing repo
cd /opt/your-app
git remote set-url origin git@github-your-app:your-org/your-repo.git
git pull
</pre>

The key lesson is: when multiple Deploy Keys exist on the same server, avoid relying on `git@github.com`. Use a project-specific SSH alias such as:

<pre>
git@github-your-app:your-org/your-repo.git
</pre>

so Git always uses the correct SSH key.