DAG

.github/workflows/ci.yml

@@ -0,0 +1,18 @@
+name: CI
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install
+        run: python -m pip install -e ".[dev]"
+      - name: Test
+        run: python -m pytest -q

.gitignore

@@ -1,4 +1,5 @@
 # Local tooling state
+.agents/
 .understand-anything/
 .vscode/
 .idea/
@@ -7,6 +8,7 @@
 __pycache__/
 *.py[cod]
 .pytest_cache/
+.pytest-tmp/
 .mypy_cache/
 .ruff_cache/
 .coverage
@@ -31,8 +33,16 @@ paper2skill_plan/
 .paper2skill-smoke-leaks.txt
 .paper2skill_desensitize_smoke.sh
 .paper2skills-sync.tar
-.agents/skills/toy-*-skill/
-.agents/skills/smoke-*-skill/
+.paper2skill-resolve/
+.paper2skill_collection/
+
+# Local planning / product notes, not release artifacts
+prd.md
+PRD.md
+next.md
+CODEX_*.md
+*_PLAN.md
+*_plan.md
 
 # Logs, temp files, and OS metadata
 *.log

CHANGELOG.md

@@ -0,0 +1,7 @@
+# Changelog
+
+## Unreleased
+
+- Added resolved repository collection as the main build input path.
+- Added workflow DAG, bio IO contract enrichment, evidence decisions, and adapter scaffolding.
+- Added dependency/API miner coverage for environment files, CLI entrypoints, R exports, and workflow engines.