fix: render research PDFs from canonical Markdown

[iamjr15]

Summary

• Render the validated research report Markdown directly into the PDF instead of flattening it into a separate section/paragraph model.
• Preserve the same headings, prose, lists, task items, tables, code, links, citations, and ordering shown in chat.
• Keep structured claim provenance internal while returning a smaller user-facing research tool result.

Architecture

The research synthesis remains the single content source. The Worker parses that bounded Markdown with a pinned GFM parser, stages the Markdown and its semantic tokens in the existing hidden artifact-input path, and the sandbox's existing React PDF runtime renders those tokens into a durable workspace/R2 PDF.

No database, storage, sandbox snapshot, or deployment-topology change is required.

Decisions Made

Decision	Choice	Alternatives considered	Reasoning
Content source	Use report.report verbatim	Rebuild a document from claims and sources	Prevents chat/PDF drift and removes synthetic appendices the user did not see in chat.
Markdown parsing	Pin marked in agent-core	Regex parsing; add runtime dependencies	Gives standards-based GFM tokens without requiring a new Daytona snapshot.
PDF runtime	Reuse React PDF and baked Liberation fonts	Browser print-to-PDF; new PDF vendor	Keeps rendering deterministic, sandbox-local, and compatible with the current document boundary.
Tool result	Return report + artifact only	Return all findings, claims, and sources	Provenance is validated internally; the smaller result makes verbatim chat presentation reliable.

Edge Cases Handled

Scenario	Handling
Long multi-page reports	A4 wrapping, widow/orphan controls, and heading presence rules prevent clipping and orphaned headings.
Nested, ordered, and task lists	Semantic list tokens retain nesting, numbering, and task state.
Comparison tables	Header, alignment, cell borders, and row-safe pagination are preserved.
Citations	Safe HTTP(S)/mailto links remain visible and clickable PDF annotations.
Inline HTML or unsafe URLs	HTML is rendered as inert text and unsupported URL schemes are not made clickable.

How to Review

1. Start with research-report-document-support.ts and research-tools.ts for the one-source data flow.
2. Review execute.ts and scripts.ts for parsing, staging, and semantic PDF rendering.
3. Review the synthesis/system prompts and README for the chat/PDF contract.

Verification

• pnpm lint
• pnpm typecheck
• pnpm turbo build --force
• pnpm deadcode
• pnpm architecture:check
• pnpm turbo skills:build
• Rendered a five-page hostile GFM fixture and visually inspected every page.
• Verified extracted text, A4 metadata, and clickable link annotations with Poppler.