OCR-to-RAG pipeline for life science screenshots

PaddleOCR with preprocessing, scispaCy NER, figure/table detection,
citation extraction, and chunked Markdown output with frontmatter.
Includes watch mode and notebook reprocessing.

.pre-commit-config.yaml

@@ -0,0 +1,27 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.2.0
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.8.0
+    hooks:
+      - id: mypy
+        additional_dependencies: [pydantic, pyyaml, typer, rich, structlog, numpy, opencv-python-headless]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: check-added-large-files
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort