v5.5.0

Added

• RDR-139: DEVONthink MCP integration. A nexus-owned bridge to DEVONthink's
  built-in MCP server, exposed through both the nx dt CLI and a new
  agent-surface MCP server. Every layer is opt-in and degrades cleanly to
  pre-RDR-139 behaviour when DEVONthink is absent (Gap 0).
  • nx dt capture <url> / --doi / --file: capture a web page, a DOI's
    open-access PDF (Unpaywall), or a loose file into DEVONthink and index it
    end to end, in one verb (Layer G). The one DT-bound verb: exits non-zero
    when DEVONthink is not running.
  • nx dt index layered opt-in flags: --link-semantic (DT-derived relates
    edges to similarity + explicit-link neighbours, Layer B), --writeback
    (stamp the nexus identity back onto the DT record: nx-indexed /
    nx-tumbler tags + a tumbler backlink, Layer F), --enrich (DT-CrossRef
    bibliographic gap-fill, lowest precedence, Layer C), --dt-content (index
    non-file-backed records from DT-extracted text, stamped
    extraction_source, Layer D), --highlights (ingest DT highlights and
    mentions, Layer E), and --extractor [auto|docling|mineru] (PDF backend,
    with the docling formula-stripped recovery).
  • nx dt highlights <tumbler|uuid>: read the ingested highlights for a record.
  • nx enrich bib --source dt: DT-CrossRef as a lowest-precedence
    bibliographic gap-filler (S2 > OpenAlex > DT-CrossRef), filling only
    still-empty bib_* fields and never overwriting a primary-backend value.
  • nx-mcp-devonthink: a new agent-surface MCP server (third sibling to
    nx-mcp / nx-mcp-catalog) advertising ~17 curated DEVONthink tools plus
    the dt_incorporate composite (Layer B + F in one agent call). It always
    spawns and gates internally on DEVONthink availability: present → the
    curated surface, absent → only a devonthink_status stub. Tools surface as
    mcp__plugin_conexus_devonthink__*.
  • New document_highlights T2 store (the eighth eager store) holding
    tumbler-keyed DEVONthink highlight / mention markdown notes, kept separate
    from document_aspects to avoid contending with the aspect worker.
• Two research proposal docs preserved under docs/proposals/
  (Beyond-Similarity-Search application, Open-Ontologies application).

Changed

• New mcp Python SDK dependency: the per-call MCP-client substrate behind the
  DEVONthink integration (Layer A), shared with the RDR-126 daemon seam.
• Excluded PyAV (av) from the resolved environment. It was pulled only by
  MinerU's unused VLM backend and vendored an ffmpeg libavdevice (62.x) that
  collided with opencv's bundled libavdevice (61.x) inside one process,
  producing the macOS objc "Class AVFFrameReceiver implemented in both ... may
  cause spurious casting failures and mysterious crashes" warning in the PDF
  extraction stack. Verified safe: the MinerU pipeline backend and Docling both
  import and run without av.

Notes

• RDR-139 Layer H (AI delegation via DEVONthink's research_topic /
  chat_response) was evaluated at its go/no-go and dropped: it produced no
  positive, material retrieval-quality delta over nexus's own nx_answer
  (live research_topic returned no usable results; chat_response is
  uncomposed generation with no citation discipline). No Layer H code shipped.
• New T2 migration document_highlights (introduced at 5.5.0). The store also
  self-creates its table on construction, so fresh installs and tests do not
  wait on the migration.