chore: consolidate root-level files into .github/ and docs/

.github/workflows/paper.yml

@@ -4,12 +4,12 @@ on:
   push:
     branches: [ main, master ]
     paths:
-      - 'paper/**'
+      - 'docs/paper/**'
       - '.github/workflows/paper.yml'
   pull_request:
     branches: [ main, master ]
     paths:
-      - 'paper/**'
+      - 'docs/paper/**'
       - '.github/workflows/paper.yml'
   workflow_dispatch:
 
@@ -34,23 +34,23 @@ jobs:
             latexmk
 
       - name: Compile LaTeX document
-        working-directory: paper
+        working-directory: docs/paper
         run: |
           latexmk -pdf -interaction=nonstopmode jquantstats.tex
 
       - name: Upload PDF artifact
         uses: actions/upload-artifact@v4
         with:
           name: jquantstats.pdf
-          path: paper/jquantstats.pdf
+          path: docs/paper/jquantstats.pdf
           retention-days: 30
 
       - name: Push PDF to paper branch
         if: github.event_name != 'pull_request'
         run: |
           git config user.name "github-actions[bot]"
           git config user.email "github-actions[bot]@users.noreply.github.com"
-          cp paper/jquantstats.pdf /tmp/jquantstats.pdf
+          cp docs/paper/jquantstats.pdf /tmp/jquantstats.pdf
           git fetch origin paper 2>/dev/null || true
           if git show-ref --verify --quiet refs/remotes/origin/paper; then
             git checkout -b paper origin/paper

.github/workflows/rhiza_quality.yml

@@ -75,7 +75,7 @@ jobs:
       - name: Run deptry
         run: make deptry
         # NOTE: make deptry is good style because it encapsulates the folders to check
-        # (e.g. src and book/marimo) and keeps CI in sync with local development.
+        # (e.g. src and docs/book/marimo) and keeps CI in sync with local development.
         # Since we have uv/uvx installed, the Makefile is optimised to use the
         # pre-installed 'uv' and 'uvx' from the system PATH.
 

.github/workflows/rhiza_release.yml

@@ -234,7 +234,7 @@ jobs:
           version: "0.10.12"
 
       - name: Generate release notes with git-cliff
-        run: uvx git-cliff --latest --output RELEASE_NOTES.md
+        run: uvx git-cliff --config .github/cliff.toml --latest --output RELEASE_NOTES.md
 
       - name: Download SBOM artifact
         # Downloads sbom.cdx.json and sbom.cdx.xml into sbom/ directory

.rhiza/.env

@@ -1,4 +1,4 @@
-MARIMO_FOLDER=book/marimo/notebooks
+MARIMO_FOLDER=docs/book/marimo/notebooks
 SOURCE_FOLDER=src
 
 # Book-specific variables

.rhiza/make.d/book.mk

@@ -42,9 +42,9 @@ _book-reports: test benchmark stress hypothesis-test
 	@[ -f "docs/reports/coverage/index.html" ]     && echo "- [Coverage Report](reports/coverage/index.html)"      >> docs/reports.md || true
 
 _book-notebooks:
-	@if [ -d "book/marimo/notebooks" ]; then \
+	@if [ -d "docs/book/marimo/notebooks" ]; then \
 	  rm -rf docs/notebooks && mkdir -p docs/notebooks; \
-	  for nb in book/marimo/notebooks/*.py; do \
+	  for nb in docs/book/marimo/notebooks/*.py; do \
 	    name=$$(basename "$$nb" .py); \
 	    printf "${BLUE}[INFO] Exporting $$nb${RESET}\n"; \
 	    abs_output="$$(pwd)/docs/notebooks/$$name.html"; \

Makefile

@@ -28,7 +28,7 @@ test-kaleido: install ## run kaleido static image export tests (requires jquants
 .PHONY: changelog
 changelog: ## generate/update CHANGELOG.md from git history using git-cliff
 	@printf "${BLUE}[INFO] Generating CHANGELOG.md with git-cliff...${RESET}\n"
-	@${UVX_BIN} git-cliff --output CHANGELOG.md
+	@${UVX_BIN} git-cliff --config .github/cliff.toml --output CHANGELOG.md
 	@printf "${GREEN}[OK] CHANGELOG.md updated.${RESET}\n"
 
 # Override the rhiza template's security target to ignore CVE-2026-4539

README.md

@@ -284,7 +284,7 @@ Contributions are welcome! Please feel free to submit a Pull Request.
 ## 📝 Citing
 
 If you use jQuantStats in academic work or research reports, please cite it using the
-[CITATIONS.bib](https://github.com/jebel-quant/jquantstats/blob/main/CITATIONS.bib) file provided in this repository:
+[CITATIONS.bib](https://github.com/jebel-quant/jquantstats/blob/main/.github/CITATIONS.bib) file provided in this repository:
 
 ```bibtex
 @software{jquantstats,