It sounds like you recently updated GitHub application and Git Shell is now broken.
Short version
To fix it
- close Git Shell
- open GitHub and let it do some post installation.
- Open Git Shell again and you should be fixed.
Long version
This just happened to me and just to make sure I follow you, you just did this
- Open Git Shell
- You are prompted to update GitHub
- After the update, Git Shell opens
Now it gives the error
git command could not be found. Please create an alias or add it to
your PATH.Warning: Could not find ssh-agent.
If this is the case, do this
- Close Git Shell
- Now open the GitHub application (not Git Shell).
This will say something along the lines of (not sure of the exact version)
GitHub is extracting git..
Let that go through the process and after it is complete, go open Git Shell and it is fixed. Just worked for me at least.