I love Autopkg and Autopkgr. They feed Munki and they keep me fed.
Sometimes Autopkg gives an error that doesn’t make sense since you don’t have enough info. Like this one:

That’s no way to make friends. Nope.
If even I understood all that… which is saying a lot. It doesn’t tell us what to do, or where to go to fix it.
Git makes sense, but maybe not in the context of Autopkgr errors. It wants us to “Git add or rm” (remove) offending items, but what does it have to do with what we’re doing at this moment? Hmm. Ok, we know that autopkgr uses autopkg which uses git but that still leaves us in the dark about what’s going on.
Drop down in terminal and poke at autopkg. That always helps.
bash-3.2$ autopkg
Usage: autopkg <verb> <options>, where <verb> is one of the following:
help (Display this help)
info (Get info about configuration or a recipe)
install (Run one or more install recipes. Example: autopkg install Firefox -- equivalent to: autopkg run Firefox.install)
list-processors (List available core Processors)
list-recipes (List recipes available locally)
make-override (Make a recipe override)
processor-info (Get information about a specific processor)
repo-add (Add one or more recipe repo from a URL)
repo-delete (Delete a recipe repo)
repo-list (List installed recipe repos)
repo-update (Update one or more recipe repos)
run (Run one or more recipes)
search (Search for recipes on GitHub.)
version (Print the current version of autopkg)
autopkg <verb> --help for more help for that verb
Looking at all that we notice that “repo-update” is most likely the autopkg command that gets activated when Autopkgr gui “update repos now” button gets clicked.

Running autopkg with repo-update option gets us a better error message.
Attempting git pull for /Users/awesome/Library/AutoPkg/RecipeRepos/
com.github.autopkg.wardsparadox-recipes...
ERROR: Pull is not possible because you have unmerged files.
Please, fix them up in the work tree, and then use 'git add/rm <file>'
as appropriate to mark resolution and make a commit.
So, at least we know now what is causing that error that Autopkgr showed us. Quick fix:
autopkg repo-delete https://github.com/autopkg/wardsparadox-recipes.git
And then we go on and pretend like nothing happened and continue on with our day, amirate? Maybe we go to the Mac Admins Slack autopkg channel and ask our colleagues, or post on the autopkg mail-list. Or we write a blog post.
More information:
The Autopkgr read me has troubleshooting tips
In the archives:
I first wrote about troubleshooting Autopkgr 2 years ago