Why was the Schnorr code removed from Bitcoin Core? I was looking for the Schnorr implementation in Bitcoin Core and was surprised to see that it was removed on Nov 2016 (commit e06e878fd7dcc99825025fa99aedb86bc7d5c29f). Why was the source code completely removed from Bitcoin Core? Was it moved to some other development repo?
The Schnorr implementation was never in Bitcoin Core. Rather it is in the libsecp256k1 library that is a subtree in Bitcoin Core. The commit you reference is actually a commit in that library which appears in Core's commit history because the subtree in Core is periodically updated with the libsecp256k1 upstream source code.
The reason for removal is explained in the pull request that removed it:

This module implemented a naive custom Schnorr signature scheme, though several flaws have been discovered with its approach since (lack of commitment to public keys, ability for 3rd parties to adapt signatures to related keys, and a multisigning API that is vulnerable to cancellation attacks, restart attacks that leak a private key to cosigners).
I have been working on a better scheme, but I don't believe this should be upstream until it's been vetted in more thorough ways. People assumed that it being included in the repository was a sign that it was final, so I'm removing it to avoid any confusion.