.gitignore
.pre-commit-config.yaml
LICENSE
MANIFEST.in
Makefile
README.md
install.sh
pyproject.toml
requirements-dev.txt
requirements.txt
./scripts/__init__.py
./scripts/canvas.py
./scripts/extract.py
./scripts/generate.py
./scripts/phd_deepread.py
./scripts/process.py
./scripts/verify.py
./scripts/templates/__init__.py
./scripts/templates/clauderules.md
./scripts/templates/critical-thinking.canvas
config/config.yaml
docs/decision-tree.md
docs/index.md
docs/workflow-guide.md
examples/example-canvas.canvas
examples/example-output.md
phd_deepread_workflow.egg-info/PKG-INFO
phd_deepread_workflow.egg-info/SOURCES.txt
phd_deepread_workflow.egg-info/dependency_links.txt
phd_deepread_workflow.egg-info/entry_points.txt
phd_deepread_workflow.egg-info/requires.txt
phd_deepread_workflow.egg-info/top_level.txt
scripts/__init__.py
scripts/batch.sh
scripts/canvas.py
scripts/extract.py
scripts/generate.py
scripts/phd_deepread.py
scripts/process.py
scripts/setup.sh
scripts/verify.py
scripts/templates/__init__.py
scripts/templates/clauderules.md
scripts/templates/critical-thinking.canvas
tests/conftest.py
tests/test_canvas.py
tests/test_extract.py
tests/test_generate.py
tests/test_verify.py