v1.11.0

MINOR release. Closes F-005 + F-019 + AUDIT-026 + AUDIT-047 + AUDIT-063

• AUDIT-073 + humanities_essay_structure deferrals. Ships the headline
  figure-auto-embed pass (walk every step's outputs/figures/ into the
  right section of paper.md before PDF compile, with a companion
  orphan-coverage audit gate). Real Reveal.js v5 + Touying-Typst slide
  compilers across 5 stock templates replace the v1.10.x skeleton. Real
  Typst poster compiler across 5 size templates replaces the legacy
  tikzposter LaTeX engine (still reachable via poster_engine: latex).
  Adds tool_audit_cross_deliverable_consistency (5-dimension check
  across paper/dashboard/slides/poster). Adds the reviewer scaffold (4
  tools + 7 bundled personas + 1 protocol) for pre-submission
  adversarial self-review with per-comment rebuttal generation and
  hand-waving audit. Adds humanities-monograph ISBN verifiers (WorldCat,
  OpenLibrary, LOC). Synthesis-pipeline config block lands in
  researcher_config.yaml (13 fields) so figure / slide / poster
  behaviour is declarative.

Deferred to v2.0.0: tool surface consolidation (search/plan/path/mem
clusters); server.py refactor (6.4K lines into focused submodules);
deprecation cleanup (hard-remove the 21 aliases that fire telemetry
today).

Added

• docs(TOOLS.md): new "Per-step audit overrides" section catalogs every override_ kwarg the server accepts (override_completeness_gate, override_dashboard_content_gate, override_discussion_coverage, override_gate, override_literature_gate, override_no_pdfs, override_rationale, allow_unfinalized_predecessor) with a tool-by-tool table and worked call snippets.
• docs(AI_GUIDE.md): new "When to override a gate" section with five worked examples (data-engineering step, literature unreachable, methodology pending, pre-publication final pass, researcher discretion) clarifying when the override path is appropriate and when fixing the underlying blocker is the right answer.
• docs: documented the override_rationale REQUIREMENT under interaction.quality_gate_policy=enforce and the workspace/logs/override_log.md line format (timestamp, tool, gate, rationale, JSON extras) so authors of the pre-submission audit have a stable contract to read.
• tests(unit): test_override_docs.py grep-asserts that every override_ kwarg present in server.py is mentioned in both docs/TOOLS.md and docs/AI_GUIDE.md, plus that override_rationale, workspace/logs/override_log.md, and the two new section anchors are present in both guides.
• Humanities monograph citation verifiers: verify_worldcat, verify_openlibrary, verify_loc in research.citations_isbn, with an verify_citation_auto dispatcher that picks the chain based on whether the citation carries an ISBN or only a DOI. Offline-safe (5s timeout, never raises). Stdlib only.
• synthesis.citations.verify_citation_entry helper that routes ISBN-bearing citations through the new monograph verifiers and falls back to Crossref for DOI-only entries.
• New synthesis/humanities_essay_structure protocol — non-IMRAD interpretive shape (thesis → contextual framing → 3-5 close readings → critical conversation → counter-argument + reply → conclusion + stakes) so humanities projects no longer fall into the IMRAD synthesis_paper template.
• New tool_humanities_essay_scaffold MCP tool — writes synthesis/paper.md with the six humanities-essay section headings + one-paragraph stubs. Idempotent: preserves substantive researcher prose on re-run.
• New router entry under synthesize intent class with humanities_essay sub-intent and triggers for "humanities essay", "close-reading essay", "write the essay", "essay structure".
• COREQ (Tong et al. 2007, 32 items) and SRQR (O'Brien et al. 2014, 21 items) reporting-standard checklists under templates/checklists/, with id / domain / item_text / guidance_short per item; closes AUDIT-026.
• tool_qualitative_select_standard (qualitative pack) — reads workspace/study_design.yaml, picks COREQ for interview/focus-group studies and SRQR otherwise, copies the matching bundled checklist into workspace/checklists/<standard>_coverage_v<N>.yaml so the walk_checklist step has a populated file to mark up.
• tests/unit/test_protocol_no_deprecated_aliases.py: regression gate that grep-walks every protocol YAML across core + every research_os_ and fails if any of the 21 deprecated alias names appears as a whole word.
• AUDIT-063: tool_synthesize accepts auto_proceed=true to process every section (methods → results → discussion → introduction → abstract) plus the full assembly in ONE call when interaction.autonomy_level=='autopilot'. Returns a structured error in manual/supervised/coaching modes. Backwards-compat: default false preserves every existing call site.
• Dashboard v2 now surfaces qualitative-pack sections (codebook table with kappa, themes hierarchy with subthemes, per-transcript saturation grid + curve, member-checking log per round) when the project's pack is detected as qualitative.
• Dashboard v2 now surfaces humanities-pack sections (apparatus criticus table, numbered close-reading anchors, critical-conversation map from citation chains, manuscript witness list with sigla) when the project's pack is detected as humanities.
• dashboard_v2.detect_active_pack(root) — resolves the active domain pack from researcher_config.yaml (pack/domain/packs) then falls back to workspace markers. Humanities wins over qualitative on tie.
• Figure auto-embed (v1.11.0 headline feature): src/research_os/tools/actions/synthesis/figure_auto_embed.py walks every numbered step's outputs/figures/ and inserts each figure into the right section of synthesis/paper.md, driven by a YAML frontmatter sidecar (section_hint, figure_priority, poster_priority, alt_text, figures_for_paper, interactive_required). Three modes: append_to_section / explicit_map / reorder. Idempotent — preserves manual placements.
• tool_paper_figures_autoembed — call directly or let tool_synthesize invoke it when synthesis.figures_auto_embed=true. Multi-paragraph captions split into headline + 'Note:' appendix. Logs every run to workspace/logs/figure_auto_embed.md.
• tool_audit_figure_coverage — BLOCKs the master quality audit when a step has a figure on disk (figures_for_paper!=false) but synthesis/paper.md does not embed it. Opt out per-step (step_summary.yaml.figures_for_paper) or per-figure (caption sidecar frontmatter).
• Cross-reference rewrite: rewrite_figure_xrefs converts bare stems ('see 01_volcano') to @fig:01_volcano cross-refs, skipping code blocks / inline code / image-link payloads / tokens already in @fig: form. Gated by synthesis.figure_xref_rewrite (default true).
• templates/step_summary.yaml.template now documents the figures_for_paper field; researcher_config.yaml ships synthesis.figures_auto_embed / figures_auto_embed_mode / figure_xref_rewrite.
• Real slide compilation engine (tool_slides_create) with two backends: engine="reveal" emits a single self-contained synthesis/slides.html using vendored Reveal.js v5 (speaker-notes plugin included), and engine="touying" emits synthesis/slides.typ against a bundled Touying-compatible Typst template and compiles to synthesis/slides.pdf via the typst CLI.
• Five stock slide templates under src/research_os/assets/slide_templates/: conference_15min, conference_5min_lightning, lab_meeting_30min (with backup section), defense_45min (35-slide chapter-arc), public_outreach (no-jargon).
• Optional print_handout=True (default) writes synthesis/slides_handout.pdf — a 2-up A4 condensed PDF with speaker notes printed beneath each slide; works for either engine via the touying handout fallback.
• Vendored Reveal.js v5 (MIT) + a minimal Touying-compatible Typst template (touying-mini, MIT) under src/research_os/assets/reveal/ and src/research_os/assets/typst_packages/touying-mini/; LICENSE + NOTICE shipped beside each.
• Real Typst poster compilation backing tool_poster_create: 5 templates (academic_36x48, academic_48x36, academic_a0_portrait, academic_a1_landscape, public_24x36), light/dark/institution_branded themes, hero figures sorted by poster_priority frontmatter, optional QR code, US-letter handout PDF.
• poster-mini Typst helper package at assets/typst_packages/poster-mini/ (poster-page / poster-header / poster-footer / poster-block / poster-headline / poster-figure / poster-bullets) plus 5 thin template wrappers at assets/poster_templates/.
• Reviewer-response scaffold: 7 bundled reviewer personas (methodology_skeptic, domain_expert, statistician, reproducibility_advocate, scope_creep_critic, novelty_critic, presentation_critic) + 4 tools (tool_reviewer_simulate, tool_rebuttal_draft, tool_reviewer_response_compile, tool_audit_reviewer_responses) + synthesis/reviewer_response protocol. Pre-submission adversarial self-review against synthesis/paper.md, per-comment rebuttal scaffolds with auto-discovered workspace evidence, compiles to response_to_reviewers.md/.pdf, audits for hand-waving + missing evidence.
• tool_audit_cross_deliverable_consistency — cross-deliverable consistency audit across paper, dashboard, slides, and poster along 5 dimensions: numeric claims (±1% tolerance), figure stems, citation keys, headline findings (Jaccard ≥ 0.30), and reproducibility footer (RO version + commit hash + build timestamp). Skipped when <2 deliverables exist; override via override_cross_deliverable + override_rationale.
• Reference-project manifests now declare a v1.11.0 contract: synthesis_deliverables (paper/slides/poster fan-out with per-deliverable tool + args + checks), cross_deliverable (title/figure-registry/citation-set consistency), and synthesis_behavior (theory-math-specific gate flags). biology_genomics_mini also declares a reviewer_simulation block (7 personas, min 30 comments).
• New reference project tests/fixtures/projects/theory_math_graph_proof/ — sub-cubic 4-colourability (corollary of Brooks 1941) with 3 inputs. Doubles as a regression target for the DEG-trigger false-positive routing bug flagged in the v1.11.0 smoke pass.
• tests/fixtures/figures/ — 4 placeholder PNGs paired with .caption.md sidecars carrying YAML frontmatter (figure_id, title, license, alt_text, source, generated_by, data_provenance) and the W3C three-part caption body shape.
• tests/fixtures/projects/humanities_ms_review/inputs/citations/monographs.yaml — 3 ISBN-bearing monograph fixtures (Bede OUP 2009, Augustine OUP 1992, Liuzza Broadview 2014) for the OpenLibrary / WorldCat / LOC verifiers.
• qualitative_interviews manifest now declares pii_redaction_expectations (must fire before synthesis; 18 HIPAA classes) and coreq_checklist (32 items walked, 28+ present) so the harness can audit the qualitative pipeline end-to-end.
• humanities_ms_review manifest now declares routing_expectations for the essay output path (project_kind=humanities + output_type=essay → humanities/output/humanities_essay_structure) and isbn_verifier_expectations (3 entries, all verifiers acceptable, network_required false for offline CI).
• tests/unit/test_v1110_reference_project_manifests.py — 23 hermetic tests pinning the new manifest contract, the graph-theory fixture presence, the caption-sidecar frontmatter shape, and the ISBN-extraction handshake against the existing _extract_isbn helper.
• Preflight check #22: check_no_deprecated_aliases_in_protocols scans every shipped protocol YAML for references to names in _DEPRECATED_ALIASES and fails the gate if any are found. Protocols must call the consolidated handler directly.
• Synthesis-config block: researcher_config.yaml ships 13 declarative knobs under synthesis: (figure auto-embed mode + xref rewrite; slide engine + template + theme + speaker_notes + handout; poster engine + template + theme + qr_url + handout). All optional with safe defaults.
• Preflight check: check_figures_for_paper_field — once any fixture ships captioned figures, the gate confirms figures_for_paper is declared at step or sidecar level.

Changed

• AUDIT-047: swept all 21 deprecated tool-name aliases from 75 shipped protocol YAMLs (74 core + wet_lab pack) and rewrote each to its canonical name via the server _ALIASES table. Also rewrote the 5 remaining sites in _router_index.yaml (sys_path_create / sys_path_abandon → sys_path; mem_methods_append / mem_decision_log → mem_log). Bumped version of every touched protocol to 1.11.0. Dispatcher still rewrites old names for back-compat, so end-user projects on prior versions are unaffected.
• synthesis/synthesis_paper protocol prose documents the new autopilot short-circuit alongside the existing 10-turn multi-turn enforcement.
• tool_dashboard_create result dict gains an active_pack field (empty string for generic STEM projects). Existing callers ignore unknown fields, so this is backwards-compatible.
• synthesis/synthesis_paper protocol final_assembly step now describes the auto-embed pass + tool_audit_figure_coverage as part of the assembly + audit loop.
• tool_slides_create inputSchema gained engine, template, theme, speaker_notes_enabled, print_handout kwargs. Legacy output_format (reveal/beamer/pdf) and audience kwargs are still accepted and silently mapped to the new engine= argument.
• tool_poster_create default engine flips from legacy tikzposter LaTeX to Typst. Set researcher_config.synthesis.poster_engine: latex (or pass engine='latex') to opt back into the tikzposter path; legacy layout / audience kwargs still route there.
• synthesis.poster_template validator enum: academic_36x48 / academic_48x36 / academic_a0_portrait / academic_a1_landscape / public_24x36. Renames a0_portrait → academic_a0_portrait and a0_landscape → academic_a1_landscape; adds public_24x36 for community-event posters.
• qualitative/output/qualitative_report_format.select_standard step now calls tool_qualitative_select_standard instead of leaving the file copy as prose; protocol bumped to 1.11.0. Qualitative pack __version__ bumped to 1.11.0.

Fixed

• Humanities smoke gap — humanities/textual/close_reading and humanities/archival/archival_research citation chains were terminal (next_protocol: null), forcing humanities synthesis through IMRAD synthesis_paper; the new structure protocol gives the chain a humanities-shape destination.

Closed

• AUDIT-073 — dashboard v2 qualitative + humanities renderers shipped (40 new unit tests).

Deferred

• Tool surface consolidation (search/plan/path/mem clusters) → v2.0.0. Aliases continue to log deprecation telemetry to .os_state/deprecations.log.
• server.py refactor (split 6.4K lines into focused submodules) → v2.0.0.
• Hard removal of the 21 _DEPRECATED_ALIASES → v2.0.0 (MAJOR — breaking).
• Wiring verify_citation_entry into the live tool_citations_verify pipeline → next minor; requires upstream mem_citations_generate to populate isbn fields on monograph entries.

Known issues (deferred to v1.11.1)

• theory_math pack — Path coercion: src/research_os/tools/actions/state/config.py:224,356 and 16 sites in audit/audit.py do root / 'workspace' without root = Path(root) coercion. Handlers called with a str root (rare in production; common in ad-hoc smoke harnesses) raise TypeError. Test suite uses Path so the gate is green; production paths from MCP transport are already Path. Fix: single-line coercion at each entry point.
• theory_math pack — pack-blind discovery: tools/actions/protocol.py:502 (list_protocols) walks only PROTOCOLS_DIR, never _pack_protocol_dirs_safe(). Symptom: sys_protocol_list(category='theory_math') returns core-only 117. Resolution via sys_protocol_get works.
• theory_math pack — router false-positive: DEG trigger (intended for "DEG analysis" / "differential expression") matches "maximum degree 3" in graph-theory prompts. Routes theory-math conjectures into guidance/analysis_plan instead of theory_math/method/proof_strategy_selection.
• theory_math pack — IMRAD-only synthesis: tool_synthesize(output_type=paper) emits [abstract, introduction, methods, results, discussion, references] even when project pack is theory_math (which prefers [introduction, preliminaries, main_theorems, proofs, discussion]). Synthesis pipeline has no hook to consult pack-supplied section schema.
• tool_synthesize — silent citation retrieval failure: e2e smoke against biology_genomics_mini shipped paper.md with citations_used=0 due to 'list index out of range' in upstream Semantic Scholar / Crossref adapter. Surfaces as cross-deliverable consistency blockers (439 numeric mismatches downstream). Tool succeeds; citations missing.
• E2E manifest — persona-name drift: tests/fixtures/projects/biology_genomics_mini/manifest.yaml lists personas (skeptical_methodologist, statistics_referee, domain_expert_neuroscience, bioinformatician_reviewer, ethics_irb_reviewer, editor_in_chief) that do not exist in src/research_os/assets/reviewer_personas/. Real persona ids: methodology_skeptic, statistician, domain_expert, reproducibility_advocate, novelty_critic, scope_creep_critic, presentation_critic. Fix: rename manifest entries to canonical ids.
• Handout naming convention: implementation writes slides_handout.pdf / poster_handout.pdf; some manifests expect slides.handout.pdf / poster.handout.pdf. Pick one and update both sides.
• Typst font warnings: every PDF compile emits non-fatal warnings for missing Linux Libertine / Times New Roman / Times. Ship a bundled fallback (e.g. New Computer Modern) or document the font install requirement.

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