Discord/Slack bot citation footer number mismatches inline citation marker when a document is cited under two different raw numbers

[NielsJorna]

Summary

When the same underlying document is retrieved and cited more than once under two different raw citation numbers within one answer, the inline [[N]] marker in the answer text can show a different number than the one listed in the bot's "Sources" footer for that same document/link — even though both point to the correct URL.

Root cause

In onyx/chat/citation_processor.py, DynamicCitationProcessor._process_citation():

# Track cited documents and create CitationInfo only for new citations
if doc_id not in self.cited_document_ids:
    self.cited_document_ids.add(doc_id)
    self.cited_documents_in_order.append(search_doc)
    citation_info_list.append(
        CitationInfo(
            citation_number=num,
            document_id=doc_id,
        )
    )

CitationInfo (and therefore anything downstream built from response.citation_info, e.g. a "Sources" footer) is only emitted the first time a document_id is cited. If the same document appears in the retrieved/ranked context at two different positions (so the model cites it under two different raw numbers, e.g. [4] and later [8]), the inline text still renders both [[4]](url) and [[8]](url) correctly (the link is baked directly into the text at each occurrence), but only the first occurrence's number ends up in citation_info. Anything built from citation_info — such as the Discord bot's source-list footer in onyx/onyxbot/discord/handle_message.py::_append_citations() — then shows that document under its first number only, which no longer matches the second inline marker.

Repro

Ask a scoped persona a question where the same doc/page is likely to surface via two different chunks/search hits (broad "what does X offer" style questions over a vendor doc set tend to trigger this). Example that reproduced it:

• Persona: a topic-scoped assistant over vendor documentation (Relevant Digital docs in this case), accessed via the Discord bot integration.
• Question: "What does Relevant Digital's platform offer for SSP management?"
• Result: the answer body contains a citation marker [8] linking to docs.relevant-digital.com/.../mapping-ad-server-and-ssp-placement-ids-..., but the rendered "Sources" footer lists that same URL as source 4. Clicking [8] inline resolves to the correct URL — the link itself isn't broken, only the visible number is inconsistent with the footer.

Impact

Cosmetic/trust issue rather than a functional break — every citation link still resolves to the correct source. But a citation number in the body that doesn't match its own footer entry is confusing and undermines confidence in the citations more broadly, especially in a low-context surface like Discord where there's no separate "Cited Sources" panel to cross-reference against (unlike the web UI).

Suggested fix direction

When collapsing/deduping citations by document_id for citation_info, either:

1. Rewrite all occurrences of the raw number(s) for a given document_id in the output text to match the single deduped number used in citation_info (similar to what onyx/chat/citation_utils.py::collapse_citations() already does for a different renumbering case), or
2. Track and expose all raw numbers that map to a given document_id, so a footer can be built that matches every inline occurrence.

Environment

• Onyx version: v4.3.0 (self-hosted, plain docker compose deployment)
• Surface: Discord bot integration (onyx/onyxbot/discord/)