feat: Cross-database transfer V2 with provenance, progress tracking, and cancellation

.coveragerc

@@ -0,0 +1,27 @@
+[run]
+source = scidk
+omit =
+    */tests/*
+    */test_*.py
+    */__pycache__/*
+    */migrations/*
+    scidk/__main__.py
+    # Exclude services not part of production MVP
+    scidk/services/commit_service.py
+    scidk/services/query_service.py
+    scidk/services/scan_index_service.py
+    scidk/services/link_migration.py
+    scidk/services/config.py
+    scidk/services/graphrag_examples.py
+    scidk/services/graphrag_llm.py
+    # Exclude experimental/optional features
+    scidk/interpreters/*
+    scidk/core/graphrag/*
+
+[report]
+precision = 2
+show_missing = True
+skip_covered = False
+
+[html]
+directory = htmlcov

.github/workflows/ci.yml

@@ -20,9 +20,19 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -e .[dev]
-      - name: Run pytest (exclude E2E)
+      - name: Run pytest with coverage (exclude E2E)
         run: |
-          python -m pytest -q -m "not e2e"
+          python -m coverage run -m pytest -q -m "not e2e"
+          python -m coverage report
+          python -m coverage xml
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          file: ./coverage.xml
+          fail_ci_if_error: false
+      - name: Check coverage threshold (50%)
+        run: |
+          python -m coverage report --fail-under=50
 
   # E2E tests temporarily disabled in CI (Feb 2026)
   # The test suite has stability issues (auth conflicts, timing, cleanup) that need dedicated attention.

.gitignore

@@ -66,3 +66,7 @@ sqlite:/tmp
 # Added here as safety net to prevent leaking into main repo
 dev/code-imports/nc3rsEDA/
 !dev/code-imports/nc3rsEDA/README.md
+/logs/
+
+# Backups are for local work, not the repository
+backups/