Gaurav Chhabra@Stefan: Thanks for letting me know the version you tried on.
I have the following: Gitolite version: gitolite3 v3.04-13-gcc9727c-dt on git 1.7.1 Git server version: git version 1.7.1 Git client version: git version 1.9.4.msysgit.2
My Git server version lags quite behind compared to yours. :) Clone of any repository is not empty because i create non-empty directories while creating any repository.
@Matthieu: You were right in saying that client can get confused if several branches point to same commit. :) Thank a ton! :) Going by what Jeff mentioned confidently, my server version (1.7.1) indeed has that flaw.
@Jeff: You've hit the nail on the head! :) Both Matthieu & you are right. I even confirmed the same by changing the content of mainline while initializing repository. SHAs indeed became different for both master and mainline. Now when i clone the repository on my local machine, it correctly points to mainline. And special thanks for pointing to the exact Git version where the flaw was fixed. :) I checked the release notes too. :)
https://git.kernel.org/cgit/git/git.git/tree/Documentation/RelNotes/1.8.4.3.txt
Thank you guys! You rock!!!