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This seems to be the most likely culprit from the logs:
error 11-Jan-2022 22:26:42 Cloning into '_libs/.phpmailer'...
error 11-Jan-2022 22:26:42 fatal: remote error:
error 11-Jan-2022 22:26:42 The unauthenticated git protocol on port 9418 is no longer supported.
error 11-Jan-2022 22:26:42 Please see https://github.blog/2021-09-01-improving-git-protocol-security-github/ for more information.
error 11-Jan-2022 22:26:42 fatal: clone of 'git://github.com/Synchro/PHPMailer.git' into submodule path '_libs/.phpmailer' failed
error 11-Jan-2022 22:26:42 Failed to recurse into submodule path 'www.website.com/.common'
I note that the server hosting Bamboo has a quite old version of git installed. git 2.7.4. None-the-less I thought I'd see if I could reproduce the problem. If the problem could be reproduced, I thought to myself, maybe I could test to see if a newer version of git would solve it. BUT when I did git clone on the main repo, which has a submodule that has git://github.com/Synchro/PHPMailer.git as a submodule, I got the following error:
Cloning into 'reponame'...
The authenticity of host 'bitbucket.org (188.8.131.52)' can't be established.
RSA key fingerprint is SHA256:zzXQOXSRBEiUtuE8AikJYKwbHaxvSc0ojez9YXaGp1A.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added 'bitbucket.org,184.108.40.206' (RSA) to the list of known hosts.
Permission denied (publickey).
fatal: Could not read from remote repository.
This suggests to me that Bamboo isn't doing git clone on the host OS. Like maybe it's doing git clone in a Docker container or something instead (altho sudo docker ps didn't show any docker containers running). ie. even if I got the git clone working in the host OS it doesn't necessarily follow that it'd start magically working in Bamboo.
I'm running Bamboo 6.10.4 build 61009 - 21 Nov 19.