The huge repo is in /etc/.git. If you don't need to retain that history, you can simply delete that git repository entirely by the following methods:
1) Delete the .git directory manually with 'rm -rf .git' - I'd consider this an emergency running out of space option. I don't know if etckeeper freaks or what, but this will definitely fix the situation. Stackoverflow reference: https://stackoverflow.com/questions/1213430/how-to-fully-delete-a-git-repository-created-with-init
2) The other option is to do the same thing using etckeeper itself. From the etckeeper site:
"Is the history recorded in that repository something you need to
preserve, or can you afford to just blow it away and check the current
/etc into the new VCS?
In the latter case, you just need to follow three steps:
etckeeper uninit # deletes /etc/.git!
You don't have to change the VCS by editing the etckeeper.conf file. If you leave the etckeeper VCS alone and do "etckeeper init", it just starts a new repo using git with the current state of the /etc directory.
Here's another reference from Turnkey Linux:
etckeeper has HUGE .git repo, how to remove???
Accepted answer by the maintainers: "Run: etckeeper uninit -f; etckeeper init"
I was running out space. I just did the step above and I deleted 15 GB of unneeded history. I think etckeeper's great to monitor the /etc directory on an ongoing basis, but I don't need 2 years of history.