I'm trying your nice program on Windows.
After importing a local repository (url http://localhost:8080/scm/git//d/git/git1/my_project/.git), i tried to clone this repository but it failed.
With Egit, I got the following message:
Cannot list the avalaible branches.
http://localhost:8080/scm/git//d/git/git1/my_project/.git/info/refs/?service=git-upload-pack not found
It thought he doesn't find the info directory as i got the following message with msysgit.
fatal: http://localhost:8080/scm/git//d/git/my_project/.git/info/refs not found: did you run git update-server-info on the server?
Then i ran the git-update-server-info and got the same message with Egit and msysgit/
Does your program use jgit instead msysgit ?
How can i configure the repository or your software to solve this issue ?