I had some trouble dealing with submodules. This is what I experienced, learned, and did to solve the issue.
Using a custom SSH URL
Let's see if our repository has submodules:
$ git submodule 9d83ae91cffb5840a5ff722e9f1dabc2d74c96ae vagrant/cookbooks (9d83ae9)
Yes, it does. Take a look at the submodule details which are stored in .gitmodules; it should look like this:
[submodule "vagrant/cookbooks"] path = vagrant/cookbooks url = email@example.com:AcmeCorporation/FlagshipProduct-cookbooks.git
Unfortunately, that's not the URL we want to use but instead we have a dedicated alias in ~/.ssh/config:
Host github HostName github.com User git IdentityFile ~/.ssh/id_rsa_github
But first, initialize the submodule (this has to be done from the repository's root path):
$ git submodule init Submodule 'vagrant/cookbooks' (firstname.lastname@example.org:AcmeCorporation/FlagshipProduct-cookbooks.git) registered for path 'vagrant/cookbooks'
Make sure that there is an URL shown between the parentheses; if there isn't, something is already wrong.
That step should have added a section to .git/config:
[…] [submodule "vagrant/cookbooks"] url = email@example.com:AcmeCorporation/FlagshipProduct-cookbooks.git
If we would have tried to update the submodule with the original SSH URL, this might fail:
$ git submodule update Permission denied (publickey). fatal: The remote end hung up unexpectedly Unable to fetch in submodule path 'vagrant/cookbooks'
Just adjust the SSH URL in .git/config as necessary (in our case, use above SSH host alias):
[…] [submodule "vagrant/cookbooks"] url = github:AcmeCorporation/FlagshipProduct-cookbooks.git
Now we can finally update the submodule:
$ git submodule update Cloning into 'vagrant/cookbooks'... remote: Counting objects: 302, done. remote: Compressing objects: 100% (216/216), done. remote: Total 302 (delta 86), reused 273 (delta 59) Receiving objects: 100% (302/302), 149.71 KiB | 198 KiB/s, done. Resolving deltas: 100% (86/86), done. Submodule path 'vagrant/cookbooks': checked out '9d83ae91cffb5840a5ff722e9f1dabc2d74c96ae'
This happened to me after I initialized the submodule:
$ git submodule update fatal: Needed a single revision Unable to find current revision in submodule path 'vagrant/cookbooks'
This is the sign that the initial checkout […] went completely wrong (I don’t know what makes this happen). Chances are that the directory exists, but is empty. Git does not seem to be able to overcome this situation, […]
So just delete the submodule's directory:
$ rm -rf vagrant/cookbooks
As pointed out in a comment to an answer on Stack Overflow, this might not be sufficient, so delete Git's internal related directory, too:
$ rm -rf .git/modules/vagrant/cookbooks
Now start again by initializing or updating the submodule.