docxology · docxology · Jun 6, 2026 · Jun 6, 2026
@@ -318,8 +318,9 @@ headers. Full surface and worked usage examples:
 
 Prerequisites: `pandoc` and a TeX distribution (`texlive-xetex` on Debian/Ubuntu,
 MacTeX on macOS). Python deps install with `uv sync` (project interpreter is
-`.venv/bin/python`, Python 3.12 per
-[`.python-version`](.python-version)). Add per-project deps with
+`.venv/bin/python`; the template targets Python 3.10+ (`requires-python` in
+[`pyproject.toml`](pyproject.toml)) and CI tests 3.10–3.12, with
+[`.python-version`](.python-version) pinning 3.12 as the local default). Add per-project deps with
 `uv run python scripts/manage_workspace.py add <package> --project <name>`. To
 generate a manuscript, follow the [Quickstart](#quickstart) at the top.
 

@@ -105,11 +105,11 @@ uv run pytest tests/infra_tests/publishing/ --collect-only -q --no-cov
 
 Result: **214** project-scope infrastructure tests collected and **381** publishing tests collected. Full behavioral gates still live in CI and in the verification commands listed by the relevant `AGENTS.md` files.
 
-**Exemplar `pytest --collect-only` totals** (2026-05-27):
+**Exemplar `pytest --collect-only` totals** (2026-05-27; `template_active_inference` re-derived 2026-06-05 after the v3.2.0 validation-spine additions):
 
 | Project | Tests collected | `src/` line+branch coverage |
 |---------|-----------------|----------------------------|
-| `template_active_inference` | 269 | 91.35 % |
+| `template_active_inference` | 343 | 91.35 % |
 | `template_autoresearch_project` | 220 | 92.81 % |
 | `template_autoscientists` | 79 | 99.59 % |
 | `template_code_project` | 196 | 98.25 % |

@@ -583,7 +583,7 @@ cp quadmath/scripts/* scripts/
 # Update dependencies
 ```
 
-**See:** [README.md Migration Section](../README.md#migration-from-quadmath)
+**See:** [README.md Migration Section](../../README.md#migration-from-quadmath)
 
 ### From Other Research Templates
 

@@ -283,7 +283,7 @@ Level 10-12: Expert Usage (1-2 months)
 ### Advanced Topics
 
 - **[Two-Layer Architecture](../architecture/two-layer-architecture.md)** - architecture guide
-- **[Modules Guide](../modules/modules-guide.md)** - Using all 14 infrastructure modules
+- **[Modules Guide](../modules/modules-guide.md)** - Using the infrastructure modules (current count in [`_generated/canonical_facts.md`](../_generated/canonical_facts.md))
 - **[Dependency management](../../README.md)** - `uv` usage and install/sync commands
 - **[CI/CD automation](../../.github/README.md)** - GitHub Actions and repository automation
 - **[Performance Optimization](../operational/config/performance-optimization.md)** - Build time optimization

@@ -5,13 +5,24 @@ infrastructure. Architecture details:
 [`architecture.md`](../core/architecture.md) and
 [`workflow.md`](../core/workflow.md).
 
-**Last verified:** 2026-05-31 (post-`v3.1.0` backlog refresh; measured
+**Last verified:** 2026-06-05 (post-`v3.2.0` release; measured
 metrics defer to [`TO-DO.md`](../../TO-DO.md) and
 [`docs/_generated/canonical_facts.md`](../_generated/canonical_facts.md)
 unless this file is re-measured)
 
 ## Completed Releases
 
+### v3.2.0 — Format, Logging, and Exemplar Hardening (2026-06-04)
+
+- added optional Pandoc-backed DOCX/EPUB rendering with per-format toggles
+  (default off)
+- extended the Active Inference validation spine with producer completeness,
+  stale-artifact checks, and dependency graph v2
+- hardened the public SIA harness boundary and re-baselined coverage gaps
+- closed GitHub supply-chain hygiene (SHA-pinned actions, `actionlint` gate,
+  guarded Dependabot automerge) and the XML-parser policy
+- see [`CHANGELOG.md`](../../CHANGELOG.md) for the full entry
+
 ### v3.1.0 — Public Exemplar / Validation-Spine Release (2026-05-30)
 
 - added the sixth public exemplar, `projects/templates/template_sia/`, plus the
@@ -90,13 +101,12 @@ and **Major**.
 - land the Active Inference gate-cache follow-up without changing the immutable
   `v3.1.0` tag
 
-### v3.2.0 — Format, Logging, and Exemplar Hardening
+### Next (open backlog)
 
-- finish terminal logging cleanup and preserve verbose file logs
-- add optional DOCX/EPUB rendering with per-format toggles
-- extend the Active Inference validation spine with producer completeness,
-  stale-artifact checks, and dependency graph v2
-- harden the public SIA harness boundary and re-baseline coverage gaps
+- finish terminal logging cleanup and preserve verbose file logs (LOG-CLEAN-1)
+- land the Active Inference gate-cache follow-up (AI-GATE-CACHE-1)
+- consolidate the defensive markdown-read helper and derive the CI project
+  matrix from the generated roster (READFILE-SAFE-1, CI-MATRIX-DYNAMIC-1)
 
 ### Next Generation (vision)
 

@@ -6,8 +6,8 @@ We actively maintain security for the following versions:
 
 | Version | Supported          |
 | ------- | ------------------ |
-| 3.1.x   | ✅ Yes             |
-| < 3.1   | ❌ No              |
+| 3.2.x   | ✅ Yes             |
+| < 3.2   | ❌ No              |
 
 ## 🐛 **Reporting a Vulnerability**
 

@@ -41,7 +41,7 @@ This index lists documentation files in the Research Project Template by categor
 ---
 
 > [!IMPORTANT]
-> **Multi-project pipeline pitfalls** (root venv deps, `matplotlib` in core deps, `project_config:` namespace, idempotency) — authoritative copy in [docs/AGENTS.md](AGENTS.md#learnings--known-issues) and [guides/new-project-setup.md](guides/new-project-setup.md#pitfall-6-project-specific-packages-absent-from-root-venv--silent-stage-4-failure).
+> **Multi-project pipeline pitfalls** (root venv deps, `matplotlib` in core deps, `project_config:` namespace, idempotency) — authoritative copy in [docs/AGENTS.md](AGENTS.md#learnings--known-issues) and [guides/new-project-setup.md](guides/new-project-setup.md#pitfall-6-root-venv).
 
 ## Topic routing (canonical → deep dives)
 
@@ -71,6 +71,7 @@ Development standards are documented in **`docs/rules/`**. The Cursor IDE entry
 - **[`rules/infrastructure_modules.md`](rules/infrastructure_modules.md)** - Infrastructure module development
 - **[`rules/testing_standards.md`](rules/testing_standards.md)** - Testing patterns
 - **[`rules/documentation_standards.md`](rules/documentation_standards.md)** - Documentation writing guide
+- **[`rules/memory_and_decision_records.md`](rules/memory_and_decision_records.md)** - Decision-memory and rationale tiering
 - **[`rules/type_hints_standards.md`](rules/type_hints_standards.md)** - Type annotation patterns
 - **[`rules/llm_standards.md`](rules/llm_standards.md)** - LLM/Ollama integration
 - **[`rules/code_style.md`](rules/code_style.md)** - Code formatting
@@ -124,6 +125,7 @@ Development standards are documented in **`docs/rules/`**. The Cursor IDE entry
 - **[architecture/adrs/002-declarative-dag-pipeline.md](architecture/adrs/002-declarative-dag-pipeline.md)** - ADR-002: Declarative DAG pipeline
 - **[architecture/adrs/003-multi-format-rendering-and-toggles.md](architecture/adrs/003-multi-format-rendering-and-toggles.md)** - ADR-003: Multi-format rendering and toggles
 - **[architecture/adrs/004-zero-mock-testing-policy.md](architecture/adrs/004-zero-mock-testing-policy.md)** - ADR-004: Zero-mock testing policy
+- **[architecture/adrs/005-decision-memory-and-adversarial-validation.md](architecture/adrs/005-decision-memory-and-adversarial-validation.md)** - ADR-005: Decision memory and adversarial validation
 - **[core/workflow.md](core/workflow.md)** - Development workflow
 - **[architecture/testing-strategy.md](architecture/testing-strategy.md)** - Testing strategy overview
 - **[architecture/discovery-export-synthesis.md](architecture/discovery-export-synthesis.md)** - Discovery and export patterns
@@ -330,6 +332,12 @@ Development standards are documented in **`docs/rules/`**. The Cursor IDE entry
 - **[prompts/comprehensive-assessment/SKILL.md](prompts/comprehensive-assessment/SKILL.md)** - Assessment and review
 - **[prompts/reproducibility-audit/SKILL.md](prompts/reproducibility-audit/SKILL.md)** - Determinism and regenerate-from-clean audit
 - **[prompts/pipeline-debugging/SKILL.md](prompts/pipeline-debugging/SKILL.md)** - Pipeline DAG-stage failure triage
+- **[prompts/academic-paper/SKILL.md](prompts/academic-paper/SKILL.md)** - Academic paper authoring
+- **[prompts/academic-paper-reviewer/SKILL.md](prompts/academic-paper-reviewer/SKILL.md)** - Academic paper review
+- **[prompts/academic-pipeline/SKILL.md](prompts/academic-pipeline/SKILL.md)** - Full academic pipeline
+- **[prompts/agentic-use/SKILL.md](prompts/agentic-use/SKILL.md)** - Agentic-use planning
+- **[prompts/deep-research/SKILL.md](prompts/deep-research/SKILL.md)** - Deep research synthesis
+- **[prompts/methods-orchestration/SKILL.md](prompts/methods-orchestration/SKILL.md)** - Methods orchestration
 
 ---
 

@@ -172,7 +172,7 @@ Reference it: \ref{fig:my_figure}
 | **Figures missing** | Run `uv run python scripts/02_run_analysis.py --project template_code_project` first |
 | **References show ??** | Check label spelling and existence |
 | **Project not discovered** | Ensure the directory is under `projects/`, has `src/` with Python files, and has `tests/`; add `manuscript/config.yaml` before rendering |
-| **Stage 4 fails silently** | Check root pyproject.toml has project deps ([details](../guides/new-project-setup.md#pitfall-6-project-specific-packages-absent-from-root-venv--silent-stage-4-failure)) |
+| **Stage 4 fails silently** | Check root pyproject.toml has project deps ([details](../guides/new-project-setup.md#pitfall-6-root-venv)) |
 | **Config warnings** | Nest custom keys under `project_config:` |
 
 ## 📊 Key Metrics