@alisio/plugin-thesis 0.1.0

package/README.es.md

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+# @alisio/plugin-thesis
+
+![Thesis Studio](./cover.webp)
+
+> English: [README.md](./README.md). Ambos README deben actualizarse en conjunto.
+
+Thesis Studio para Alisio. Te entrevista, planifica la investigación, investiga cada sección hasta
+formar una biblioteca de evidencia verificada, redacta solo a partir de evidencia aprobada, revisa el
+resultado de forma independiente y compone una tesis universitaria en el idioma que elijas. El código
+determinista decide cada compuerta que pueda; los agentes hijos solo proponen. La política proviene de
+paquetes versionados y con fuentes, y las reglas de tu institución siempre prevalecen.
+
+## Requisitos
+
+- Node.js 22.16 o superior y `@alisio/sdk` 0.3 a 0.6. No se necesitan credenciales.
+- Motor de PDF: ejecuta `/thesis:setup` una vez para instalar en la caché el Typst fijado (con SHA-256
+  verificado). Sin Typst, `/thesis:build` recurre a Chrome o Chromium sin interfaz, y
+  `/thesis:build --html` no necesita ninguno.
+- La investigación consulta OpenAlex, Crossref y arXiv (orígenes fijos). Define
+  `ALISIO_THESIS_CONTACT_EMAIL` para usar sus «polite pools»; se lee solo del entorno y nunca se
+  almacena ni se registra.
+
+## Instalación
+
+```sh
+alisio install npm:@alisio/plugin-thesis
+```
+
+## Inicio rápido
+
+```text
+/thesis:init                 # crea thesis/ e inicia la entrevista (primero el idioma)
+/thesis:design               # redacta research/protocol.md; aprueba las compuertas humanas A y B
+/thesis:outline              # redacta outline/outline.json; aprueba la compuerta OUTLINE
+/thesis:research SEC-03      # busca, verifica, valora; lee evidence/dossiers/SEC-03.md
+/thesis:draft SEC-03         # redacta, edita y revisa la sección; tú la apruebas
+/thesis:build                # genera el PDF (o /thesis:build --html)
+```
+
+`/thesis:status` muestra la fase, las compuertas y el siguiente paso, y `/thesis:next` lo ejecuta. En
+una sesión sin interfaz, `/thesis:init` devuelve las preguntas con sus opciones y la sintaxis exacta de
+`/thesis:answer`: las respuestas son pares `id=valor` separados por espacios o saltos de línea, o un
+único objeto JSON; el texto libre va en `<id>:text=...`.
+
+## Arquitectura
+
+![Arquitectura](./assets/architecture.svg)
+
+Los comandos, las herramientas y la CLI llegan a un único coordinador en TypeScript. Este ejecuta
+agentes hijos de solo lectura, acepta únicamente JSON validado, escribe él mismo todos los archivos,
+ejecuta las comprobaciones y entrega un `ThesisDocument` neutral al puerto de renderizado. Un adaptador
+DOCX futuro está previsto y no se incluye todavía.
+
+## Ciclo de vida
+
+![Ciclo de vida](./assets/lifecycle.svg)
+
+La tesis avanza desde la entrevista y el diseño, pasando por tres compuertas humanas, a un ciclo por
+sección y luego a la revisión, la finalización (compuerta humana C) y una compilación PDF/A.
+
+### El ciclo por sección
+
+1. `/thesis:research SEC-id`: busca, verifica y valora; tú validas el dossier.
+2. `/thesis:draft SEC-id`: el redactor recibe solo evidencia citable y devuelve Markdown con anclas de
+   afirmaciones. El código valida claves de cita, anclas, etiquetas y figuras, escribe
+   `chapters/NN-slug.md` y `claims/claims.jsonl` y ejecuta las comprobaciones. Luego el editor cambia
+   solo la redacción: el código compara citas, anclas, números, etiquetas y fórmulas antes y después y
+   rechaza cualquier cambio. Tú apruebas, pides una revisión o vuelves a la investigación. La
+   aprobación compila las secciones aprobadas.
+3. Cuando todas las secciones están aprobadas, la tesis entra en revisión: `/thesis:review all`,
+   corrige o descarta los hallazgos y luego `/thesis:finalize`.
+
+Los resúmenes se redactan al final; la declaración de uso de IA, la dedicatoria y los agradecimientos no
+requieren investigación; la bibliografía se genera desde la biblioteca.
+
+## Comandos
+
+| Comando | Propósito |
+| --- | --- |
+| `/thesis:init [dir] [--lang <bcp47>] [--presentation]` | Crea el espacio de trabajo y ejecuta la entrevista |
+| `/thesis:answer -- <id=valor ...\|json>` | Responde las preguntas pendientes sin interfaz |
+| `/thesis:status` | Fase, compuertas, secciones y siguiente paso |
+| `/thesis:next` | Ejecuta el siguiente paso recomendado |
+| `/thesis:check [gate...]` | Ejecuta las comprobaciones y escribe `build/check-report.json` |
+| `/thesis:design`, `/thesis:outline` | Redactan el protocolo o el esquema y piden las compuertas humanas |
+| `/thesis:approve <destino> [-- notas]` | Registra una aprobación: `A`, `B`, `OUTLINE`, `C`, `SEC-id`, `FND-id`, `ETH-id`, `norms`, `style:id` |
+| `/thesis:revise <destino> -- <comentarios>` | Envía comentarios al rol responsable del destino |
+| `/thesis:research <SEC-id\|next> [-- ...]` | Investiga una sección; `-- add <DOI o URL; título; año; tipo>` verifica una fuente que ya tienes |
+| `/thesis:draft <SEC-id\|next> [-- comentarios]` | Redacta, edita, comprueba y pide aprobación |
+| `/thesis:figure <SEC-id> -- <solicitud>` | Redacta un gráfico, diagrama o tabla (devuelve el Markdown a insertar) |
+| `/thesis:review [SEC-id\|all]` | Revisión independiente; los hallazgos van a `reviews/FND-*.json` |
+| `/thesis:finalize` | G9 y G10, compuerta humana C, compilación PDF/A, `build/submission/` |
+| `/thesis:build [full\|approved\|SEC-id] [--pdfa] [--html]` | Genera el PDF o la vista previa HTML |
+| `/thesis:setup` | Instala el motor Typst fijado (con suma de verificación) |
+| `/thesis:pack new\|list\|check\|explain` | Crea, lista, comprueba y explica paquetes de políticas |
+| `/thesis:style new\|list\|check` | Crea, lista y comprueba estilos de cita y perfiles |
+| `/thesis:norms import -- <texto de guía\|URL\|ruta>` | Convierte una guía o rúbrica en un paquete del espacio de trabajo (tú lo apruebas) |
+| `/thesis:doctor` | Informa motores, paquetes incluidos y paquetes de políticas; no cambia nada |
+
+Los argumentos usan `<destino> -- <texto>`. Las URL de guías solo se obtienen mediante una herramienta
+`web_fetch` del anfitrión.
+
+## Herramientas
+
+| Herramienta | Propósito |
+| --- | --- |
+| `thesis_scholar_search` | Busca en OpenAlex, Crossref o arXiv |
+| `thesis_scholar_resolve` | Resuelve un DOI o identificador a un registro académico |
+| `thesis_status` | Resume el espacio de trabajo |
+| `thesis_check` | Ejecuta las comprobaciones deterministas |
+| `thesis_build` | Genera la tesis |
+
+## CLI
+
+```sh
+alisio-thesis check [dir] [--json] [--gate G0,G7] [--no-write]
+alisio-thesis build [dir] [full|approved|SEC-id] [--pdfa] [--json]
+alisio-thesis bib [dir] [--check]
+alisio-thesis doctor [--json]
+alisio-thesis style list|check [dir] [--json]
+```
+
+`check` termina con 0 si ninguna comprobación falla, 1 si alguna falla y 2 ante errores de uso o de
+entorno, por lo que sirve en CI y en hooks de git.
+
+## Estructura del espacio de trabajo
+
+```text
+thesis/
+  thesis.yaml              # ficha del proyecto (editable por personas)
+  compliance-profile.json  # reglas resueltas con su rastro de ruleId
+  research/protocol.md     outline/outline.json
+  evidence/                # library.jsonl, rejected.jsonl, search-log.jsonl, dossiers/
+  claims/claims.jsonl      bibliography/references.bib   (generado, nunca se edita a mano)
+  chapters/  chapters/annexes/
+  figures/{charts,diagrams,images}/   data/
+  styles/                  # .csl, .profile.yaml y fixtures/ del espacio de trabajo
+  policy/  policy-packs/   # ajustes simples y paquetes del espacio de trabajo
+  reviews/FND-*.json
+  build/                   # generado, ignorado por git: PDF, HTML, informe, submission/
+.alisio/thesis/state.json  # estado del ciclo de vida
+```
+
+## Dialecto Markdown
+
+| Elemento | Sintaxis |
+| --- | --- |
+| Etiqueta de sección | `## Metodología {#sec-methodology}` |
+| Cita | `[@perez2021]`, `[@perez2021, p. 17]`, `[@a2020; @b2021]`; narrativa `@perez2021` |
+| Referencia cruzada | `@fig-x`, `@tbl-x`, `@eq-x`, `@sec-x` |
+| Matemáticas | en línea `$x^2$`; en bloque `$$ ... $$ {#eq-x}` |
+| Figura | `![Leyenda. Fuente: ...](figures/charts/x.vl.json){#fig-x width=100%}` (`.vl.json`, `.mmd`, `.svg`, `.png`, `.jpg`) |
+| Tabla | Tabla GFM seguida de `Table: Leyenda {#tbl-x}` |
+| Nota al pie | `[^1]` |
+| Ancla de afirmación | `<!-- claim:c3 -->` al inicio del párrafo (la consumen las comprobaciones) |
+
+El HTML crudo, el Typst crudo y los atributos desconocidos son errores `HYG-001`. Los gráficos son
+especificaciones Vega-Lite cuyo `data.url` nombra un archivo `.csv` o `.json` dentro de `thesis/data/`;
+el plugin los renderiza con colores definidos por la paleta. Los diagramas Mermaid usan un tema generado
+a partir de la paleta.
+
+## Idiomas
+
+La tesis se escribe en cualquier idioma BCP-47 que elijas. Las etiquetas generadas (portada, títulos,
+leyendas) se incluyen en inglés y español; los demás idiomas usan las etiquetas en inglés. `LNG-001`
+detecta inglés, español, portugués y francés. El resumen en un segundo idioma es opcional.
+
+## Estilos de cita, estilos del espacio de trabajo y perfiles
+
+Estilos CSL incluidos: `apa-7`, `ieee` y un `icontec-ntc1486-2022` provisional (notas al pie numeradas
+con Ibid./Op. cit.; no existe un CSL oficial, así que confírmalo con tu programa). Coloca tus propios
+`<id>.csl` y `<id>.profile.yaml` en `thesis/styles/` y selecciona el id en `thesis.yaml`. Los perfiles son
+YAML declarativo con un esquema cerrado (`extends` de un perfil incluido y luego márgenes, tipografías,
+títulos, leyendas, numeración de páginas y portada); las claves desconocidas fallan con `PRF-001`.
+`/thesis:style check` los valida (`CSL-001`, `PRF-001`, `CSL-010`). `/thesis:style new` redacta un estilo
+a partir de una guía y te pide aprobarlo antes de usarlo.
+
+## Paquetes de políticas
+
+![Resolución de políticas](./assets/policy-resolution.svg)
+
+Los paquetes incluidos `global` y `CO`, tus paquetes del espacio de trabajo y los ajustes simples
+alimentan un único resolutor. Este ordena las reglas por nivel y alcance, reemplaza una regla incluida
+solo con `overrides: true` y registra el rastro de `ruleId` de cada valor en el perfil de cumplimiento.
+
+Se amplía sin modificar el plugin. Agrega paquetes en `thesis/policy-packs/` (`international/`,
+`countries/`, `institutions/<CC>/<slug>/` con `faculties/` y `programs/`, `writing/`), cada uno con un
+`manifest.yaml` (`packId`, `scope`, `version`, y opcionalmente `appliesWhen` y `extends`).
+`/thesis:pack new <scope> <id>` genera un paquete comentado, `/thesis:pack check` lo valida (`PCK-001` a
+`PCK-004`, `PCK-010`) y `/thesis:pack explain <ruleId|valor>` imprime el rastro de resolución. Para
+ajustes simples sin manifiesto, coloca archivos de reglas en `thesis/policy/` (`institution.yaml`,
+`faculty.yaml`, `program.yaml`, `rubric.yaml`, `writing-*.yaml`). Las reglas con
+`basis: secondary_source` conviene confirmarlas con tu programa.
+
+## Evidencia
+
+![Pipeline de evidencia](./assets/evidence-pipeline.svg)
+
+El código verifica los candidatos de las fuentes académicas (resolución de DOI, similitud de título,
+estado de retractación, dominios oficiales) antes de que un auditor los valore. Solo se pueden citar los
+registros de la biblioteca, y los candidatos rechazados quedan en `evidence/rejected.jsonl`.
+
+## Comprobaciones deterministas
+
+Las comprobaciones son funciones puras agrupadas en las compuertas G0 a G10: ficha y políticas (`BRF`,
+`POL`, `CSL`, `PRF`), diseño y esquema (`DSN`, `OUT`), evidencia (`EVD`), citas y afirmaciones (`CIT`,
+`CLM`), referencias cruzadas, figuras y matemáticas (`XRF`, `FIG`, `MTH`), idioma y redacción (`LNG`,
+`WRT`, `HYG`), ética y uso de IA (`ETH`, `POL-AI`), compilación (`BLD`), revisión (`REV`) y finalización
+(`FIN`). Ejecuta `/thesis:check` o `alisio-thesis check`.
+
+## Sin Typst
+
+`/thesis:build` prefiere el Typst fijado. Si no hay ninguno, recurre a Chrome o Chromium sin interfaz
+(`ALISIO_THESIS_CHROME` elige un binario, `off` desactiva el recurso) y avisa de que el diseño difiere:
+las citas usan una aproximación integrada del estilo seleccionado, y PDF/A requiere Typst.
+`/thesis:build --html` escribe `build/thesis.html`. Todo lo que usa la página está incluido en el
+paquete; Chrome se ejecuta con un perfil temporal y todas las solicitudes de red bloqueadas.
+
+## Agentes y habilidades
+
+Ocho agentes de solo lectura (coordinador, metodólogo, bibliotecario, auditor de evidencia, arquitecto,
+redactor, editor, revisor) y quince habilidades específicas se incluyen en `.agents/`. Solo el código del
+coordinador escribe archivos.
+
+## Seguridad
+
+- Toda ruta aportada por el usuario o por un agente hijo permanece dentro del espacio de trabajo; la
+  salida de los agentes hijos no es confiable: es JSON validado y acotado.
+- Sin shell: los procesos usan arreglos de argumentos y tiempos límite. Typst se ejecuta con su raíz en
+  el directorio de compilación, nunca con Typst crudo desde Markdown, y solo con paquetes incluidos.
+- Vega se ejecuta con `vega-interpreter` (sin generación de código) y solo lee `thesis/data/`.
+- El uso de red se limita a los orígenes académicos, la descarga de `/thesis:setup` y las herramientas
+  del anfitrión.
+- El estado y los archivos generados se escriben de forma atómica con permisos restrictivos.
+
+## Licencias
+
+MIT. Los paquetes Typst incluidos, las bibliotecas de navegador (Paged.js, KaTeX, Mermaid) y sus
+licencias figuran en `THIRD_PARTY_NOTICES.md`. Los estilos `apa.csl` e `ieee.csl` provienen del
+repositorio Citation Style Language bajo CC BY-SA 3.0; `apa.csl` es un derivado modificado y documentado
+(una corrección de macro de fecha) y conserva la misma licencia. Las reglas de los paquetes de políticas
+citan sus fuentes.

package/README.md

@@ -0,0 +1,235 @@
+# @alisio/plugin-thesis
+
+![Thesis Studio](./cover.webp)
+
+> Español: [README.es.md](./README.es.md). The two READMEs must be updated together.
+
+Thesis Studio for Alisio. It interviews you, plans the research, researches each section into a
+verified evidence library, drafts from approved evidence only, reviews the result independently and
+typesets a university thesis in the language you choose. Deterministic code decides every gate it
+can; child agents only propose. Policy comes from versioned, sourced packs, and your institution's
+rules always win.
+
+## Requirements
+
+- Node.js 22.16 or newer and `@alisio/sdk` 0.3 to 0.6. No credentials are needed.
+- PDF engine: run `/thesis:setup` once to install the pinned Typst into the cache (SHA-256
+  verified). Without Typst, `/thesis:build` falls back to headless Chrome or Chromium, and
+  `/thesis:build --html` needs neither.
+- Research queries OpenAlex, Crossref and arXiv (fixed origins). Set `ALISIO_THESIS_CONTACT_EMAIL`
+  to use their polite pools; it is read from the environment only and never stored or logged.
+
+## Install
+
+```sh
+alisio install npm:@alisio/plugin-thesis
+```
+
+## Quickstart
+
+```text
+/thesis:init                 # create thesis/ and start the interview (language first)
+/thesis:design               # draft research/protocol.md; approve Human Gates A and B
+/thesis:outline              # draft outline/outline.json; approve the OUTLINE gate
+/thesis:research SEC-03      # search, verify, appraise; read evidence/dossiers/SEC-03.md
+/thesis:draft SEC-03         # write, edit and check the section; you approve it
+/thesis:build                # build the PDF (or /thesis:build --html)
+```
+
+`/thesis:status` shows the phase, gates and the next step, and `/thesis:next` runs it. In a headless
+session `/thesis:init` returns the questions with their options and the exact `/thesis:answer`
+syntax: answers are `id=value` pairs separated by spaces or new lines, or one JSON object; free text
+goes in `<id>:text=...`.
+
+## Architecture
+
+![Architecture](./assets/architecture.svg)
+
+Commands, tools and the CLI reach one TypeScript coordinator. It runs read-only child agents, accepts
+only validated JSON, writes every file itself, runs the checks and hands a neutral `ThesisDocument`
+to the renderer port. A future DOCX adapter is planned and is not shipped.
+
+## Lifecycle
+
+![Lifecycle](./assets/lifecycle.svg)
+
+The thesis moves from intake and design through three human gates to a per-section loop, then
+review, finalization (Human Gate C) and a PDF/A build.
+
+### The per-section loop
+
+1. `/thesis:research SEC-id`: search, verify, appraise; you validate the dossier.
+2. `/thesis:draft SEC-id`: the writer receives only citable evidence and returns Markdown with claim
+   anchors. Code validates citation keys, anchors, labels and figures, writes `chapters/NN-slug.md`
+   and `claims/claims.jsonl` and runs the checks. The editor then changes wording only: code compares
+   citations, claim anchors, numbers, labels and math before and after and rejects any change. You
+   approve, ask for a revision or go back to research. Approval builds the approved sections.
+3. When every section is approved the thesis enters review: `/thesis:review all`, fix or dismiss
+   findings, then `/thesis:finalize`.
+
+Abstracts are drafted last; the AI-use declaration, dedication and acknowledgments need no research;
+the bibliography is generated from the library.
+
+## Commands
+
+| Command | Purpose |
+| --- | --- |
+| `/thesis:init [dir] [--lang <bcp47>] [--presentation]` | Create the workspace and run the interview |
+| `/thesis:answer -- <id=value ...\|json>` | Answer pending interview questions headlessly |
+| `/thesis:status` | Phase, gates, sections and the next step |
+| `/thesis:next` | Run the next recommended step |
+| `/thesis:check [gate...]` | Run deterministic checks, write `build/check-report.json` |
+| `/thesis:design`, `/thesis:outline` | Draft the protocol or the outline and ask the human gates |
+| `/thesis:approve <target> [-- notes]` | Record an approval: `A`, `B`, `OUTLINE`, `C`, `SEC-id`, `FND-id`, `ETH-id`, `norms`, `style:id` |
+| `/thesis:revise <target> -- <feedback>` | Send feedback to the role that owns the target |
+| `/thesis:research <SEC-id\|next> [-- ...]` | Research a section; `-- add <DOI or URL; title; year; type>` verifies a source you have |
+| `/thesis:draft <SEC-id\|next> [-- feedback]` | Draft, edit, check and ask for approval |
+| `/thesis:figure <SEC-id> -- <request>` | Draft a chart, diagram or table (returns Markdown to insert) |
+| `/thesis:review [SEC-id\|all]` | Independent review; findings go to `reviews/FND-*.json` |
+| `/thesis:finalize` | G9 and G10, Human Gate C, PDF/A build, `build/submission/` |
+| `/thesis:build [full\|approved\|SEC-id] [--pdfa] [--html]` | Build the PDF or the HTML preview |
+| `/thesis:setup` | Install the pinned Typst engine (checksum verified) |
+| `/thesis:pack new\|list\|check\|explain` | Create, list, check and explain policy packs |
+| `/thesis:style new\|list\|check` | Author, list and check citation styles and profiles |
+| `/thesis:norms import -- <guide text\|URL\|path>` | Turn a guide or rubric into a workspace pack (you approve it) |
+| `/thesis:doctor` | Report engines, vendored packages and packs; changes nothing |
+
+Arguments use `<target> -- <text>`. Guide URLs are fetched only through a host `web_fetch` tool.
+
+## Tools
+
+| Tool | Purpose |
+| --- | --- |
+| `thesis_scholar_search` | Search OpenAlex, Crossref or arXiv |
+| `thesis_scholar_resolve` | Resolve a DOI or identifier to a scholarly record |
+| `thesis_status` | Summarize the workspace |
+| `thesis_check` | Run the deterministic checks |
+| `thesis_build` | Build the thesis |
+
+## CLI
+
+```sh
+alisio-thesis check [dir] [--json] [--gate G0,G7] [--no-write]
+alisio-thesis build [dir] [full|approved|SEC-id] [--pdfa] [--json]
+alisio-thesis bib [dir] [--check]
+alisio-thesis doctor [--json]
+alisio-thesis style list|check [dir] [--json]
+```
+
+`check` exits 0 when no check fails, 1 when a check fails and 2 on usage or environment errors, so it
+works in CI and git hooks.
+
+## Workspace layout
+
+```text
+thesis/
+  thesis.yaml              # project brief (human-editable)
+  compliance-profile.json  # resolved rules with their ruleId trail
+  research/protocol.md     outline/outline.json
+  evidence/                # library.jsonl, rejected.jsonl, search-log.jsonl, dossiers/
+  claims/claims.jsonl      bibliography/references.bib   (generated, never hand-edited)
+  chapters/  chapters/annexes/
+  figures/{charts,diagrams,images}/   data/
+  styles/                  # workspace .csl, .profile.yaml, fixtures/
+  policy/  policy-packs/   # simple overrides and workspace packs
+  reviews/FND-*.json
+  build/                   # generated, git-ignored: PDF, HTML, check report, submission/
+.alisio/thesis/state.json  # lifecycle state
+```
+
+## Markdown dialect
+
+| Construct | Syntax |
+| --- | --- |
+| Section label | `## Methodology {#sec-methodology}` |
+| Citation | `[@perez2021]`, `[@perez2021, p. 17]`, `[@a2020; @b2021]`; narrative `@perez2021` |
+| Cross-reference | `@fig-x`, `@tbl-x`, `@eq-x`, `@sec-x` |
+| Math | inline `$x^2$`; display `$$ ... $$ {#eq-x}` |
+| Figure | `![Caption. Source: ...](figures/charts/x.vl.json){#fig-x width=100%}` (`.vl.json`, `.mmd`, `.svg`, `.png`, `.jpg`) |
+| Table | GFM pipe table followed by `Table: Caption {#tbl-x}` |
+| Footnote | `[^1]` |
+| Claim anchor | `<!-- claim:c3 -->` at paragraph start (consumed by checks) |
+
+Raw HTML, raw Typst and unknown attributes are `HYG-001` errors. Charts are Vega-Lite specs whose
+`data.url` names a `.csv` or `.json` file under `thesis/data/`; the plugin renders them itself with
+palette-driven colors. Mermaid diagrams take a theme generated from the palette.
+
+## Languages
+
+The thesis is written in any BCP-47 language you choose. Generated labels (cover, headings, captions)
+ship in English and Spanish; other languages use the English labels. `LNG-001` detects English,
+Spanish, Portuguese and French. A second-language abstract is optional.
+
+## Citation styles, workspace styles and profiles
+
+Shipped CSL styles: `apa-7`, `ieee` and a provisional `icontec-ntc1486-2022` (numbered footnotes with
+Ibid./Op. cit.; no official CSL exists, so confirm it with your program). Put your own `<id>.csl` and
+`<id>.profile.yaml` in `thesis/styles/` and select the id in `thesis.yaml`. Profiles are declarative
+YAML with a closed schema (`extends` a shipped profile, then override margins, fonts, headings,
+captions, page numbers, cover); unknown keys fail `PRF-001`. `/thesis:style check` validates them
+(`CSL-001`, `PRF-001`, `CSL-010`). `/thesis:style new` drafts a style from a guide and asks you to
+approve it first.
+
+## Policy packs
+
+![Policy resolution](./assets/policy-resolution.svg)
+
+Shipped `global` and `CO` packs and your workspace packs and simple overrides feed one resolver. It
+orders rules by level and scope, replaces a shipped rule only with `overrides: true` and records the
+`ruleId` trail of every value in the compliance profile.
+
+Extend it without modifying the plugin. Add packs under `thesis/policy-packs/` (`international/`,
+`countries/`, `institutions/<CC>/<slug>/` with `faculties/` and `programs/`, `writing/`), each with a
+`manifest.yaml` (`packId`, `scope`, `version`, optional `appliesWhen` and `extends`). `/thesis:pack new
+<scope> <id>` scaffolds a commented pack, `/thesis:pack check` validates it (`PCK-001` to `PCK-004`,
+`PCK-010`) and `/thesis:pack explain <ruleId|value>` prints a resolution trail. For simple overrides
+without a manifest, put rule files in `thesis/policy/` (`institution.yaml`, `faculty.yaml`,
+`program.yaml`, `rubric.yaml`, `writing-*.yaml`). Rules marked `basis: secondary_source` should be
+confirmed with your program.
+
+## Evidence
+
+![Evidence pipeline](./assets/evidence-pipeline.svg)
+
+Candidates from the scholarly sources are verified by code (DOI resolution, title similarity,
+retraction status, official domains) before an auditor appraises them. Only library records can be
+cited, and rejected candidates stay in `evidence/rejected.jsonl`.
+
+## Deterministic checks
+
+Checks are pure functions grouped in gates G0 to G10: brief and policy (`BRF`, `POL`, `CSL`, `PRF`),
+design and outline (`DSN`, `OUT`), evidence (`EVD`), citations and claims (`CIT`, `CLM`), cross-references,
+figures and math (`XRF`, `FIG`, `MTH`), language and writing (`LNG`, `WRT`, `HYG`), ethics and AI use
+(`ETH`, `POL-AI`), build (`BLD`), review (`REV`) and finalization (`FIN`). Run `/thesis:check` or
+`alisio-thesis check`.
+
+## Without Typst
+
+`/thesis:build` prefers the pinned Typst. When none is available it falls back to headless Chrome or
+Chromium (`ALISIO_THESIS_CHROME` selects a binary, `off` disables the fallback) and warns that the
+layout differs: citations use a built-in approximation of the selected style, and PDF/A needs Typst.
+`/thesis:build --html` writes `build/thesis.html`. Everything the page uses is vendored; Chrome runs
+with a temporary profile and every network request blocked.
+
+## Agents and skills
+
+Eight read-only agents (coordinator, methodologist, librarian, evidence auditor, architect, writer,
+editor, reviewer) and fifteen focused skills ship in `.agents/`. Only the coordinator code writes
+files.
+
+## Security
+
+- Every user- or child-supplied path stays inside the workspace; child output is untrusted JSON,
+  validated and capped.
+- No shell: processes use argv arrays and timeouts. Typst runs with its root set to the build
+  directory, never from raw Typst in Markdown, and only vendored packages.
+- Vega runs with `vega-interpreter` (no code generation) and reads only `thesis/data/`.
+- Network use is limited to the scholarly origins, the `/thesis:setup` release download and host tools.
+- State and generated files are written atomically with restrictive modes.
+
+## Licensing
+
+MIT. Vendored Typst packages, browser libraries (Paged.js, KaTeX, Mermaid) and their licenses are
+listed in `THIRD_PARTY_NOTICES.md`. The `apa.csl` and `ieee.csl` styles come from the Citation Style
+Language repository under CC BY-SA 3.0; `apa.csl` is a documented modified derivative (a date-macro fix)
+and keeps the same license. Policy-pack rules cite their sources.

package/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,94 @@
+# Third-party notices
+
+This package vendors two Typst packages, three browser libraries for the Chrome/HTML output and three CSL styles, and depends on seven npm packages. Each keeps its own
+license; the full license texts ship next to the vendored files.
+
+## Vendored Typst packages (`typst-packages/preview/`)
+
+These are copied unmodified from the Typst package registry and loaded offline through
+`--package-path`; nothing is downloaded at build time.
+
+| Package | Version | License | Files |
+| --- | --- | --- | --- |
+| mitex | 0.2.7 | Apache-2.0 | `typst-packages/preview/mitex/0.2.7/` (license: `LICENSE`) |
+| merman | 0.3.0 | MIT OR Apache-2.0 | `typst-packages/preview/merman/0.3.0/` (licenses: `LICENSE`, `THIRD_PARTY_NOTICES.md`, `THIRD_PARTY_LICENSES/`) |
+
+merman bundles the following components in its WebAssembly plugin. Their license texts are in
+`typst-packages/preview/merman/0.3.0/THIRD_PARTY_LICENSES/`:
+
+| Component | Version | License |
+| --- | --- | --- |
+| cose-base 1.x | 1.0.3 | MIT |
+| cose-base 2.x | 2.2.0 | MIT |
+| Cytoscape.js | 3.34.0 | MIT |
+| cytoscape.js-cose-bilkent | 4.1.0 | MIT |
+| cytoscape.js-fcose | 2.2.0 | MIT |
+| d3-shape | 3.2.0 | ISC |
+| Dagre | 2.0.2 | MIT |
+| DOMPurify | 3.4.13 | Apache-2.0 OR MPL-2.0 |
+| fmin | 0.0.4 | BSD-3-Clause |
+| Graphlib | 2.2.4 | MIT |
+| layout-base 1.x | 1.0.2 | MIT |
+| layout-base 2.x | 2.0.1 | MIT |
+| Mermaid | 11.16.1 | MIT |
+| rough-rs (roughr) | 0.12.0 | MIT |
+| Rough.js | 4.6.6 | MIT |
+| sanitize-url | 7.1.1 | MIT |
+| @upsetjs/venn.js | 2.0.0 | MIT |
+| ZenUML Core | 3.50.1 | MIT |
+| Eclipse Layout Kernel | 0.9.1 | EPL-2.0 |
+| elkjs | 0.9.3 | EPL-2.0 |
+| wasm-minimal-protocol | 0.2.0 | Unlicense |
+
+The Eclipse Layout Kernel and elkjs are distributed under the Eclipse Public License 2.0; their
+source is available from https://github.com/eclipse-elk/elk and https://github.com/kieler/elkjs.
+
+## Vendored browser libraries (`templates/html/vendor/`)
+
+Used only by the Chrome PDF fallback and the HTML preview (`/thesis:build --html`). They are copied
+unmodified from the npm tarballs listed below (versions pinned) and loaded from the local build
+directory; the page never fetches anything from the network. KaTeX is also evaluated in Node (in an
+isolated `vm` context) to typeset formulas before the page is written. Each folder keeps its upstream
+license text.
+
+| Library | Version | License | Source tarball (SHA-256) | Vendored file (SHA-256, bytes) |
+| --- | --- | --- | --- | --- |
+| Paged.js | 0.4.3 | MIT | `pagedjs-0.4.3.tgz` (`a79baaa94d15cf952e6327950fa886ba7533bdce92194b677d9d1b4cce6c17c5`) | `pagedjs/paged.polyfill.min.js` (`f44e35a6d5106d819c3415fd38591de04d3834343c14e50a562b84257e204692`, 503181) |
+| KaTeX | 0.19.0 | MIT | `katex-0.19.0.tgz` (`d8e49f2fea6eeed7cdae2cf4fd48e2f1d348758aa9e5740715e4533c2c96d1ee`) | `katex/katex.min.js` (`103a53763cc033bba8d175bf3f0ba597c3505c9b6747dd3f2c7bc2a6bfcc8ae7`, 272868); `katex/katex.min.css` (`d4ab5b8ee16989b070cdb0ea24bd6ad48fc8df1b787f280f29d3ae4f959f2c00`, 24793); `katex/fonts/*.woff2` (20 files, 263888 bytes; the CSS lists the woff and ttf fallbacks, which are not shipped) |
+| Mermaid | 11.16.1 | MIT | `mermaid-11.16.1.tgz` (`ebd9885111092c78cefc79a76f6c1dc34ed5b834b02ae8f338227ce79c003de4`) | `mermaid/mermaid.min.js` (`18327bef70d96fb505fe7287d9f6a7362ebf07ff6576ddfaffb1a06f3e1a2954`, 3566058) |
+
+`mermaid.min.js` is the upstream single-file bundle; it includes the components that Mermaid declares
+as dependencies (among them d3, dagre-d3-es, Cytoscape and its layouts, DOMPurify, KaTeX, khroma, marked,
+roughjs, stylis, ts-dedent, uuid, dayjs, es-toolkit, @braintree/sanitize-url and @upsetjs/venn.js)
+under MIT, ISC, BSD-3-Clause, Apache-2.0 or MPL-2.0 terms; the bundle's own comments and the
+tables for the same Mermaid release in the merman section above name them. citeproc-js is not used:
+the HTML output formats citations with a small built-in formatter.
+
+## Vendored citation styles (`styles/`)
+
+| File | Source | License |
+| --- | --- | --- |
+| `apa.csl` | https://github.com/citation-style-language/styles (2026-10-04); **modified derivative**: the `date` and `date-issued-month-day` macros print month and day with their own prefix so that sources without a month no longer render `(2012,)` under Typst/Hayagriva. The change is noted in the style's `<info>` and header comment | CC BY-SA 3.0 |
+| `ieee.csl` | https://github.com/citation-style-language/styles (copied unmodified, 2026-10-04) | CC BY-SA 3.0 |
+| `icontec-ntc1486-2022.csl` | Written for this package from public NTC 1486:2022 library guides (provisional) | CC BY-SA 3.0 |
+
+Each style keeps its `<rights>` notice. The license text is in `styles/LICENSE-CSL`; the
+golden fixtures under `styles/fixtures/` are renderings of these styles and share their license.
+
+## Typst CLI (not bundled)
+
+The Typst command-line compiler (Apache-2.0, https://github.com/typst/typst) is not part of this
+package. `/thesis:setup` downloads the pinned release from GitHub after verifying its SHA-256, or
+you point `ALISIO_THESIS_TYPST` at your own copy.
+
+## npm dependencies
+
+| Package | License |
+| --- | --- |
+| markdown-it | MIT |
+| markdown-it-footnote | MIT |
+| yaml | ISC |
+| vega | BSD-3-Clause |
+| vega-lite | BSD-3-Clause |
+| vega-interpreter | BSD-3-Clause |
+| d3-dsv | ISC |

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