In the process of cloning a repo through my company proxy server through sysinternal I can see the it tried to write the git repository but failed. However, the .git directory was created but mostly with empty directories.
I have set up my proxy server configuration with "git config --globlal http.proxy ..." and "git config --global https.proxy ...".
Since I connected to git (I was prompted to enter my account/password), I know the proxy setup works.
From Sysinternal I can see the errors as
Query Open C:\Users\myUser\https:\github.com\myGitAccount\source.git\.git FAST IO DISALLOWED
CreateFile C:\Users\myUser\https:\github.com\myGitAccount\source.git\.git NAME INVALID Denied Access: Read Attributes. Disposition:
Github verified that the repo is fine.
A git clone for an https accessed GitHub repo should be:
git clone https://github.com/aUserName/aRepoName.git
And it should takes place in a session where HOME is defined if you want to cache your GitHub credentials, as mentioned in "Git - How to use .netrc file on windows to save user and password".
For the proxy, see also "Syncing with github".