How to fix SSH / Git connections after windows update broke them? Issue seems to be related to ssh-agent

Question

I use Windows 10 / PyCharm / GitHub Desktop as my developer environment.

I use ssh keys to access my remote git repository. Everything on my computer functioned perfectly a week ago, but now it does not.

I have Github Desktop installed, and that is not affected. I can use Github Desktop to pull/push/etc from the repository. My issue is with the command line tools & with the git tool integrations into PyCharm (my IDE).

I have my RSA keys in my $HOME/.ssh/ folder and a config file in $HOME/.ssh/config that has not changed...but now everytime I attempt to do a "git fetch" command from CMD/Powershell/Git Bash I get prompted for a password. This password prompt is showing up because it is NOT reading my SSH config file and it is NOT using my RSA key!!!!

I know this is the case because I can "fix" the issue in Git Bash by executing the following commands:

eval $(ssh-agent -s)
ssh-add C:/Users/MyUsername/.ssh/id_rsa

After executing those commands, everything works perfectly in Git Bash.

I have spent HOURS googling this issue and restarrting my SSH services, rebooting my computer, resintalling my IDE, and even attempting to do a system restore back to last week....NONE of them fix the issue.

WHY do I need to add my ssh keys to Git Bash everytime I open it? It seems like it is not reading the keys/config file from the default $HOME/.ssh directory. How do I fix this? What is going on? I'm about ready to throw this computer out the window!!!

Restarting Software - Nothing Rebooting Computer - Nothing Copying $HOME/.ssh/config to multiple directories as suggested by google search results - Nothing Using Github Desktop - WORKS, but I want the CLI tools / integrated Git flow in PyCharm to work! Using Git Bash with "eval $(ssh-agent -s); ssh-add" workaround - WORKS but very cumbersome. Why doesn't it remember the keys session to session? Why do I need to execute every time?

Answer 1

Hacky solution:

I used ssh -Tvvv git@gitlab both before and after executing the "eval $(ssh-agent -s); ssh-add " workaround and loaded them into Beyondcompare and noticed that the tool was trying to grab keys from C:\SPB_Data directory in the 'before' (I have no idea what this directory is) and C:\Users\MyUsername 'after':

debug1: Next authentication method: publickey
debug1: Trying private key: /c/SPB_Data/.ssh/id_rsa
debug3: no such identity: /c/SPB_Data/.ssh/id_rsa: No such file or directory

So I simply copied all the files from C:\Users\Myusername.ssh into C:\SPB_Data.ssh and then everything worked.

The root-cause of this issues seems to be the installation of Allegro / Cadence software which OVERWRITES the $HOME environment variable and causes OpenSSH to read from that folder instead of the Windows home folder.