Add user-configurable citation styles to RWA. Users pick a default style during setup (stored in .rwa-user-config.yaml), override per-project (in project-config.yaml), and each project gets a self-contained copy of its .csl file. Ship ~10 common styles in a csl/ directory; allow downloading additional styles from the Zotero Styles Repository on demand.

Author: andre-inter-collab-llc

.github/agents/academic-writer.agent.md

@@ -84,6 +84,11 @@ Before creating a new cite-bearing document, check the target project's `project
 For reports, manuscripts, and protocols that include citations:
 - Populate YAML frontmatter with the known author metadata
 - Include `bibliography` and `csl` fields unless the user explicitly wants a citation-free output
+- **Resolve the CSL citation style using this priority chain:**
+  1. Project's `project-config.yaml` → `research_assistant.output_defaults.csl`
+  2. User's `.rwa-user-config.yaml` → `default_citation_style` (+ `.csl` extension)
+  3. Fallback: `apa.csl`
+- Verify the resolved `.csl` file exists in the project directory. If it does not, use `bib_copy_csl_to_project` to copy it from the shared `csl/` library.
 - Add an editable RWA disclosure in the Methods section when AI-assisted workflow details are relevant
 - Add an acknowledgments / AI-disclosure section with ICMJE-compliant language
 - When Research Workflow Assistant (RWA) is cited in Methods or Acknowledgments, use [@vanzyl2026rwa] and add the matching BibTeX entry from `templates/rwa-citation.bib` to `references.bib`

.github/agents/project-manager.agent.md

@@ -6,6 +6,7 @@ description: >
   meeting notes, and timeline management.
 tools:
   - project-tracker
+  - bibliography-manager
 ---
 
 # Project Manager Agent
@@ -163,10 +164,11 @@ At natural project checkpoints, proactively ask:
 1. Ask the researcher about their project (title, timeline, type, and who should be listed as authors on project outputs)
 2. If `.rwa-user-config.yaml` contains `default_author`, offer to use it as the starting author profile for the project and let the researcher edit or override any field
 3. Collect any additional project authors and store them in `project-config.yaml` under `research_assistant.authors`
-4. Initialize tracking via `project-tracker`, preserving structured author metadata when the tool supports it
-5. Suggest a phase structure based on the project type
-6. Help define initial milestones and tasks
-7. Offer to generate the first brief ("starting point" baseline)
+4. **Citation style**: Read `default_citation_style` from `.rwa-user-config.yaml`. Ask: "Your default citation style is {style}. Should I use it for this project, or would you prefer a different style?" If the user picks a different style, check if it exists in `csl/` — if not, use `bib_download_csl_style` to fetch it. Then use `bib_copy_csl_to_project` to copy the chosen `.csl` file into the new project directory. Set `output_defaults.csl` in the project's `project-config.yaml` to match.
+5. Initialize tracking via `project-tracker`, preserving structured author metadata when the tool supports it
+6. Suggest a phase structure based on the project type
+7. Help define initial milestones and tasks
+8. Offer to generate the first brief ("starting point" baseline)
 
 ### Ongoing Management
 

.github/agents/research-planner.agent.md

@@ -6,6 +6,7 @@ description: >
 tools:
   - prisma-tracker
   - project-tracker
+  - bibliography-manager
 ---
 
 # Research Planner Agent
@@ -42,6 +43,7 @@ Guide the researcher through creating a study protocol, adapting to the study ty
 - Risk of bias assessment (which tool for which study types)
 - Synthesis plan (narrative, meta-analysis, or both)
 - Use the `templates/systematic-review/protocol.qmd` template
+- When creating any `.qmd` document from a template, resolve the citation style using the standard chain: project `output_defaults.csl` → user `default_citation_style` → `apa.csl` fallback. Ensure the resolved `.csl` file exists in the project directory.
 
 **Observational Study Protocol:**
 - Study design (cohort, case-control, cross-sectional)

.github/agents/setup.agent.md

@@ -14,6 +14,7 @@ tools:
   - zotero-local
   - project-tracker
   - prisma-tracker
+  - bibliography-manager
 ---
 
 # RWA Setup Agent
@@ -265,7 +266,43 @@ default_author:
 
 If `default_author` already exists, show which fields are already set and ask before overwriting them.
 
-**Transition**: "Your default author profile is saved. Would you like to create your first project?"
+**Transition**: "Your default author profile is saved. Let's choose your preferred citation style."
+
+## Stage 7.5 — Default Citation Style
+
+Ask the user to choose their preferred citation / referencing style. This becomes the default for all new projects (overridable per project).
+
+1. **List bundled styles**: Use the `bib_list_csl_styles` tool from the bibliography-manager MCP server to show the available styles. Present them in a clear table:
+
+   | ID | Style | Type |
+   |----|-------|------|
+   | `apa` | APA 7th edition | Author-date |
+   | `vancouver` | Vancouver / NLM (numbered) | Numbered |
+   | `vancouver-superscript` | Vancouver (superscript) | Superscript numbered |
+   | `american-medical-association` | AMA 11th edition | Superscript numbered |
+   | `bmj` | BMJ | Numbered |
+   | `nature` | Nature | Numbered |
+   | `national-library-of-medicine` | NLM / Citing Medicine 2nd ed. | Numbered |
+   | `ieee` | IEEE | Numbered (bracketed) |
+   | `harvard-cite-them-right` | Harvard (Cite Them Right 12th ed.) | Author-date |
+   | `chicago-author-date-17th-edition` | Chicago 17th (author-date) | Author-date |
+   | `chicago-fullnote-bibliography` | Chicago 18th (notes & bibliography) | Footnotes |
+
+2. **Ask**: "Which citation style do you prefer? Enter the style ID from the list above, or type a custom style ID from the [Zotero Style Repository](https://www.zotero.org/styles) (over 10 000 styles available). Press Enter to accept the default (APA)."
+
+3. **If the user enters a bundled style ID**: Confirm the selection.
+4. **If the user enters a custom style ID** not in the bundled list: Use the `bib_download_csl_style` tool to download it from the Zotero Style Repository. If the download fails (style not found), inform the user and ask them to try again or browse https://www.zotero.org/styles.
+5. **Default**: If the user presses Enter or says "default", use `apa`.
+
+Save the selection to `.rwa-user-config.yaml` under `default_citation_style`:
+
+```yaml
+default_citation_style: vancouver-superscript
+```
+
+If `default_citation_style` already exists, show the current value and ask if the user wants to change it.
+
+**Transition**: "Your default citation style is saved. Would you like to create your first project?"
 
 ## Stage 8 — First Project Setup (Optional)
 
@@ -316,7 +353,12 @@ Use the `project-tracker` server to:
 
 4. Create `ai-contributions-log.md` in the project directory with the standard template header.
 
-5. Create `project-config.yaml` in the project directory with:
+5. **Copy the citation style file** into the project directory. Ask the user:
+   - "Should I use your default citation style ({default_citation_style from .rwa-user-config.yaml}) for this project, or would you like a different style?"
+   - Use `bib_copy_csl_to_project` to copy the chosen `.csl` file from the shared `csl/` library into the project directory.
+   - If the user picks a style not yet in the library, use `bib_download_csl_style` first, then copy it.
+
+6. Create `project-config.yaml` in the project directory with:
    ```yaml
    research_assistant:
      tracking_location: self
@@ -338,10 +380,11 @@ Use the `project-tracker` server to:
                   url: {organization URL if provided}
          output_defaults:
             bibliography: references.bib
-            csl: apa.csl
+            csl: {chosen style}.csl
             include_rwa_methods_disclosure: true
             include_rwa_acknowledgments: true
    ```
+   Note: `output_defaults.csl` must match the CSL filename that was copied into the project directory in step 5.
 
 **Transition**: "Your project is set up! Here is a summary of everything we configured."
 
@@ -376,6 +419,9 @@ Print a clear summary:
 - Affiliation: {organization or "not configured"}
 - ORCID: {configured/skipped}
 
+### Default Citation Style
+- Style: {style title} ({style ID}) / not configured (defaults to APA)
+
 ### First Project
 - {Project title} (created at {path}) / No project created yet
 

.github/agents/systematic-reviewer.agent.md

@@ -58,7 +58,8 @@ Ask the user which framework fits their question. If they are unsure, recommend
 Before searching, prompt the user to develop or register a protocol:
 
 1. Suggest drafting a protocol using the `templates/systematic-review/protocol.qmd` template
-2. Mention PROSPERO registration (for systematic reviews) or OSF preregistration (for scoping reviews)
+2. When creating the protocol `.qmd` file, resolve the citation style using the standard chain: project `output_defaults.csl` → user `default_citation_style` → `apa.csl` fallback. Ensure the resolved `.csl` file exists in the project directory (copy it from `csl/` if needed using `bib_copy_csl_to_project`).
+3. Mention PROSPERO registration (for systematic reviews) or OSF preregistration (for scoping reviews)
 3. Document the planned methods: databases to search, inclusion/exclusion criteria, screening process, data extraction plan, synthesis method
 
 ### Phase 3: Search Strategy Development

.github/copilot-instructions.md

@@ -224,6 +224,22 @@ Agents should:
 - Recommend [Quarto CLI](https://quarto.org/docs/get-started/) installation when rendering is needed
 - See `docs/posit-quarto-guide.md` for the full Posit/Quarto ecosystem guide
 
+### Citation Style Defaults
+
+Citation formatting uses **CSL (Citation Style Language)** files processed by Pandoc citeproc. The repository ships a shared style library in `csl/` with common styles pre-bundled. Additional styles can be downloaded on demand from the [Zotero Style Repository](https://www.zotero.org/styles) (10,000+ styles) via the `bib_download_csl_style` tool.
+
+**Resolution chain** (agents must follow this priority order):
+1. **Project config** — `output_defaults.csl` in `project-config.yaml`
+2. **User config** — `default_citation_style` in `.rwa-user-config.yaml`
+3. **Fallback** — `apa` (APA 7th edition)
+
+**Rules for all agents:**
+- Each project directory gets its own copy of the `.csl` file (for portability). Use `bib_copy_csl_to_project` to copy from the shared library.
+- When instantiating a Quarto template, resolve the CSL style via the chain above and substitute the `csl:` field in the YAML front matter.
+- Never hardcode a path back to the repo-root `csl/` directory in project documents — always use a local copy.
+- If the resolved style is not in the shared library, download it first with `bib_download_csl_style`.
+- See `csl/README.md` for the full list of bundled styles and instructions for adding more.
+
 ### Diagram and Table Defaults
 
 **Diagrams:** The default diagram tool is **Mermaid**, which is natively supported by Quarto via ` ```{mermaid} ` code blocks (no extensions or installs required). Use Mermaid for:

csl/README.md

@@ -0,0 +1,47 @@
+# Citation Style Library
+
+This directory contains [Citation Style Language (CSL)](https://citationstyles.org/) files used by Quarto/Pandoc to format in-text citations and bibliographies.
+
+## Bundled Styles
+
+| File | Style | Type | Common In |
+|------|-------|------|-----------|
+| `apa.csl` | APA Style 7th edition | Author-date | Psychology, education, social sciences |
+| `vancouver.csl` | Vancouver (NLM, citation-sequence) | Numbered | Medicine, biomedical sciences |
+| `vancouver-superscript.csl` | Vancouver (superscript numbers) | Superscript numbered | Medicine, clinical journals |
+| `american-medical-association.csl` | AMA Manual of Style 11th edition | Superscript numbered | US medical journals |
+| `bmj.csl` | BMJ | Numbered | BMJ family journals |
+| `nature.csl` | Nature | Numbered | Nature family journals |
+| `national-library-of-medicine.csl` | NLM/Citing Medicine 2nd edition | Numbered | Library science, government reports |
+| `ieee.csl` | IEEE Reference Guide | Numbered (bracketed) | Engineering, computer science |
+| `harvard-cite-them-right.csl` | Cite Them Right 12th ed. (Harvard) | Author-date | UK universities, general |
+| `chicago-author-date-17th-edition.csl` | Chicago 17th edition (author-date) | Author-date | History, humanities, social sciences |
+| `chicago-fullnote-bibliography.csl` | Chicago 18th edition (notes & bibliography) | Footnotes | History, arts, humanities |
+
+## Using a Style
+
+In your Quarto (`.qmd`) document YAML front matter:
+
+```yaml
+bibliography: references.bib
+csl: vancouver-superscript.csl
+```
+
+The CSL file should be in the same directory as your `.qmd` file (RWA copies the appropriate file into each project directory during project creation).
+
+## Adding More Styles
+
+Over 10,000 styles are available from the [Zotero Style Repository](https://www.zotero.org/styles). To add a new style:
+
+1. **Via RWA**: Ask any agent to download a citation style — it will use the `download_csl_style` tool to fetch and save it automatically.
+2. **Manually**: Download the `.csl` file from [zotero.org/styles](https://www.zotero.org/styles) and place it in this directory.
+
+## Configuration
+
+- **User default**: Set `default_citation_style` in `.rwa-user-config.yaml` (configured during `@setup`).
+- **Per-project override**: Set `output_defaults.csl` in your project's `project-config.yaml`.
+- **Resolution chain**: Project config → User config → `apa` (fallback).
+
+## License
+
+All CSL styles in this directory are sourced from the [Citation Style Language](https://github.com/citation-style-language/styles) project and are licensed under the [Creative Commons Attribution-ShareAlike 3.0 Unported (CC BY-SA 3.0)](https://creativecommons.org/licenses/by-sa/3.0/) license.