Is there a place to submit pull requests for git-annex?
I've made a small change to the docs, adding html anchors to enable hyperlinks to docs for specific config settings, on a branch here: https://github.com/notestaff/git-annex/tree/is-doc-add-html-anchors-for-config-vars
The thing to do is to go to https://git-annex.branchable.com/todo and make a post there. Include either the url to the git repo to pull from, or paste in a git patch to apply.
I took a look at your html anchors patch. After applying it and running "make mans", the man/git-annex.1 page had broken formatting around those html anchors. It would need some additional change to Build/mdwn2man to make it deal with them.