I've cloned a repository using the windows command prompt, but the only reason I know it exists and cloned succesfully is that I can see it with git bash.
In both the command prompt and in windows explorer, it is hidden.
I have went to the Folder and Search options and I had it already set to show hidden files, so Im out of ideas to why they dont appear there.
I also wanted to understand why sometime I could find my .git repo folder in Windows 7 file explorer on some but not other repos. I found it to be Windows Virtual Store was being implemented whenever my git repo was in what was a protected area, say working on a plugin for an application in C:\Program Files. Here is another question asking how to find such re-directed files.
How to detect file redirection to the Windows VirtualStore?
It seems git-bash, git-gui is automatically picking up these Virtual Store files, while file-explorer doesn't. Anyway the .git folder for Virtual Store is located:
%HOMEDRIVE%%HOMEPATH%\AppData\Local\VirtualStore\
Under an identical folder structure as from the root folder to your git repo instance.