Deploy the FileAnnotations extension to the beta cluster.
Storage in Wikibase? Or T107595: [RFC] Multi-Content Revisions?
I'm at the iannotate conference right now -- is there documentation on the annotation format you are using? (Or anything in particular you need help with?)
Note that the W3C annotation spec includes an API component: https://www.w3.org/TR/annotation-protocol/
It would be great if we could publish our annotations in this standard way.
But, if this takes a while, we should at least start by embedding the annotations in our HTML (which seems easier to implement): https://www.w3.org/TR/annotation-html/ (specifically https://www.w3.org/TR/annotation-html/#mixing-rdfa-with-embedded-rdf-content)
Note that the wikidata folks seem likely to be able to publish annotations as a proper JSON-LD object without too much effort: T44063: [Epic] Provide a plain linked data interface for accessing entities. It may still be easier to embed them in HTML, but we haven't actually had positive experiences with embedded RDFa on the Parsoid side -- mostly that nobody pays attention to it. The tooling for JSON-LD looks a little better.
Since the 2016/2017 FileAnnotations prototype work is now quite outdated and both Wikidata and Commons have new features and design plans (like moving new features to Vue.js on Commons), and the extension is not actively under development, the best thing to do is close these tasks and create new ones when/if there's a team available to pick up development on this feature.