feat(gitlab): comprehensive integration alignment with GitHub

.github/workflows/ci.yml

@@ -96,7 +96,7 @@ jobs:
           PYTHONPATH: ${{ github.workspace }}/apps/backend
         run: |
           source .venv/bin/activate
-          pytest ../../tests/ -v --cov=. --cov-report=xml --cov-report=term-missing --cov-fail-under=10
+          pytest ../../tests/ __tests__/ -v --cov=. --cov-report=xml --cov-report=term-missing --cov-fail-under=10
 
       - name: Upload coverage to Codecov
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'

.husky/pre-commit

@@ -1,36 +1,55 @@
 #!/bin/sh
 
 # =============================================================================
-# GIT WORKTREE ENVIRONMENT CLEANUP
+# GIT WORKTREE CONTEXT HANDLING
 # =============================================================================
-# Git automatically sets GIT_DIR (and CWD to the working tree root) before
-# running hooks -- even in worktrees. We do NOT need to manually parse .git
-# files or export GIT_DIR/GIT_WORK_TREE.
+# When running in a worktree, we need to preserve git context to prevent HEAD
+# corruption. However, we must also CLEAR these variables when NOT in a worktree
+# to prevent cross-worktree contamination (files leaking between worktrees).
 #
-# However, external tools (IDEs, agents, parent shells) may leave stale
-# GIT_DIR/GIT_WORK_TREE values in the environment. If these point to a
-# different repo or worktree, git commands in this hook would target the
-# wrong repository. Unsetting them lets git re-resolve the correct values
-# from the working directory.
+# The bug: If GIT_DIR/GIT_WORK_TREE are set from a previous worktree session
+# and this hook runs in the main repo (where .git is a directory, not a file),
+# git commands will target the wrong repository, causing files to appear as
+# untracked in the wrong location.
+#
+# Fix: Explicitly unset these variables when NOT in a worktree context.
 # =============================================================================
-unset GIT_DIR
-unset GIT_WORK_TREE
+
+if [ -f ".git" ]; then
+  # We're in a worktree (.git is a file pointing to the actual git dir)
+  # Use -n with /p to only print lines that match the gitdir: prefix, head -1 for safety
+  WORKTREE_GIT_DIR=$(sed -n 's/^gitdir: //p' .git | head -1)
+  if [ -n "$WORKTREE_GIT_DIR" ] && [ -d "$WORKTREE_GIT_DIR" ]; then
+    # Resolve to absolute path to avoid issues with relative gitdir paths
+    # Use pwd -P to canonicalize symlinks (resolves symlinked directories)
+    WORKTREE_GIT_DIR=$(cd "$(dirname "$WORKTREE_GIT_DIR")" && pwd -P)/$(basename "$WORKTREE_GIT_DIR")
+    export GIT_DIR="$WORKTREE_GIT_DIR"
+    export GIT_WORK_TREE="$(pwd -P)"
+  else
+    # .git file exists but is malformed or points to non-existent directory
+    # CRITICAL: Clear any inherited GIT_DIR/GIT_WORK_TREE to prevent cross-worktree leakage
+    unset GIT_DIR
+    unset GIT_WORK_TREE
+  fi
+else
+  # We're in the main repo (.git is a directory)
+  # CRITICAL: Clear any inherited GIT_DIR/GIT_WORK_TREE to prevent cross-worktree leakage
+  unset GIT_DIR
+  unset GIT_WORK_TREE
+fi
 
 # =============================================================================
 # SAFETY CHECK: Detect and fix corrupted core.worktree configuration
 # =============================================================================
-# core.worktree lives in the SHARED .git/config (not per-worktree). If any
-# process accidentally writes it (e.g., running `git init` with a leaked
-# GIT_WORK_TREE), ALL repos and worktrees see the wrong working tree root,
-# causing files from one worktree to "leak" into others.
-#
-# This check runs from both main repo and worktree contexts since the config
-# is shared and corruption can happen from either.
-CORE_WORKTREE=$(git config --get core.worktree 2>/dev/null || true)
-if [ -n "$CORE_WORKTREE" ]; then
-  echo "Warning: Detected corrupted core.worktree setting ('$CORE_WORKTREE'), removing it..."
-  if ! git config --unset core.worktree 2>/dev/null; then
-    echo "Warning: Failed to unset core.worktree. Manual intervention may be needed."
+# If core.worktree is set in the main repo's config (pointing to a worktree),
+# this indicates previous corruption. Fix it automatically.
+if [ ! -f ".git" ]; then
+  CORE_WORKTREE=$(git config --get core.worktree 2>/dev/null || true)
+  if [ -n "$CORE_WORKTREE" ]; then
+    echo "Warning: Detected corrupted core.worktree setting, removing it..."
+    if ! git config --unset core.worktree 2>/dev/null; then
+      echo "Warning: Failed to unset core.worktree. Manual intervention may be needed."
+    fi
   fi
 fi
 
@@ -162,39 +181,48 @@ if git diff --cached --name-only | grep -q "^apps/backend/.*\.py$"; then
   fi
 
   # Run pytest (skip slow/integration tests and Windows-incompatible tests for pre-commit speed)
-  # Run from repo root (not apps/backend) so tests that use Path.resolve() get correct CWD.
-  # PYTHONPATH includes apps/backend so imports resolve correctly.
+  # Use subshell to isolate directory changes and prevent worktree corruption
   echo "Running Python tests..."
   (
-    # Tests to skip: graphiti (external deps), merge_file_tracker/service_orchestrator/worktree/workspace (Windows path/git issues)
-    # Also skip tests that require optional dependencies (pydantic structured outputs)
-    # Also skip gitlab_e2e (e2e test sensitive to test-ordering env contamination, validated by CI)
-    IGNORE_TESTS="--ignore=tests/test_graphiti.py --ignore=tests/test_merge_file_tracker.py --ignore=tests/test_service_orchestrator.py --ignore=tests/test_worktree.py --ignore=tests/test_workspace.py --ignore=tests/test_finding_validation.py --ignore=tests/test_sdk_structured_output.py --ignore=tests/test_structured_outputs.py --ignore=tests/test_gitlab_e2e.py"
+    cd apps/backend || exit 1
+    # Tests to skip and reasons why:
+    # - test_graphiti.py: Requires external Graphiti service (not available in CI)
+    # - test_merge_file_tracker.py: Windows path handling issues (uses backslash assumptions)
+    # - test_service_orchestrator.py: Windows git path issues (worktree handling)
+    # - test_worktree.py: Windows git path issues (worktree handling)
+    # - test_workspace.py: Windows path handling issues (uses backslash assumptions)
+    # - test_finding_validation.py: Requires pydantic structured outputs (optional dependency)
+    # - test_sdk_structured_output.py: Requires pydantic structured outputs (optional dependency)
+    # - test_structured_outputs.py: Requires pydantic structured outputs (optional dependency)
+    # TODO: Re-evaluate exclusions periodically as Windows support improves and deps change
+    IGNORE_TESTS="--ignore=../../tests/test_graphiti.py --ignore=../../tests/test_merge_file_tracker.py --ignore=../../tests/test_service_orchestrator.py --ignore=../../tests/test_worktree.py --ignore=../../tests/test_workspace.py --ignore=../../tests/test_finding_validation.py --ignore=../../tests/test_sdk_structured_output.py --ignore=../../tests/test_structured_outputs.py"
+
     # Determine Python executable from venv
     VENV_PYTHON=""
-    if [ -f "apps/backend/.venv/bin/python" ]; then
-      VENV_PYTHON="apps/backend/.venv/bin/python"
-    elif [ -f "apps/backend/.venv/Scripts/python.exe" ]; then
-      VENV_PYTHON="apps/backend/.venv/Scripts/python.exe"
+    if [ -f ".venv/bin/python" ]; then
+      VENV_PYTHON=".venv/bin/python"
+    elif [ -f ".venv/Scripts/python.exe" ]; then
+      VENV_PYTHON=".venv/Scripts/python.exe"
     fi
 
-    # -k "not windows_path": skip tests using fake Windows paths that break
-    # Path.resolve() on macOS/Linux. These are validated by CI on all platforms.
     if [ -n "$VENV_PYTHON" ]; then
       # Check if pytest is installed in venv
       if $VENV_PYTHON -c "import pytest" 2>/dev/null; then
-        PYTHONPATH=apps/backend $VENV_PYTHON -m pytest tests/ -v --tb=short -x -m "not slow and not integration" -k "not windows_path" $IGNORE_TESTS
+        PYTHONPATH=. $VENV_PYTHON -m pytest ../../tests/ -v --tb=short -x -m "not slow and not integration" $IGNORE_TESTS
       else
         echo "Warning: pytest not installed in venv. Installing test dependencies..."
-        $VENV_PYTHON -m pip install -q -r tests/requirements-test.txt
-        PYTHONPATH=apps/backend $VENV_PYTHON -m pytest tests/ -v --tb=short -x -m "not slow and not integration" -k "not windows_path" $IGNORE_TESTS
+        if $VENV_PYTHON -m pip install -q -r ../../tests/requirements-test.txt; then
+          PYTHONPATH=. $VENV_PYTHON -m pytest ../../tests/ -v --tb=short -x -m "not slow and not integration" $IGNORE_TESTS
+        else
+          echo "Warning: Failed to install test dependencies. Skipping tests."
+        fi
       fi
-    elif [ -d "apps/backend/.venv" ]; then
+    elif [ -d ".venv" ]; then
       echo "Warning: venv exists but Python not found in it, using system Python"
-      PYTHONPATH=apps/backend python -m pytest tests/ -v --tb=short -x -m "not slow and not integration" -k "not windows_path" $IGNORE_TESTS
+      PYTHONPATH=. python -m pytest ../../tests/ -v --tb=short -x -m "not slow and not integration" $IGNORE_TESTS
     else
       echo "Warning: No .venv found in apps/backend, using system Python"
-      PYTHONPATH=apps/backend python -m pytest tests/ -v --tb=short -x -m "not slow and not integration" -k "not windows_path" $IGNORE_TESTS
+      PYTHONPATH=. python -m pytest ../../tests/ -v --tb=short -x -m "not slow and not integration" $IGNORE_TESTS
     fi
   )
   if [ $? -ne 0 ]; then
@@ -251,7 +279,7 @@ if git diff --cached --name-only | grep -q "^apps/frontend/"; then
     # Dependencies available - run full frontend checks
     # Use subshell to isolate directory changes and prevent worktree corruption
     (
-      cd apps/frontend
+      cd apps/frontend || exit 1
 
       # Run lint-staged (handles staged .ts/.tsx files)
       npm exec lint-staged

apps/backend/.gitignore

@@ -62,9 +62,6 @@ Thumbs.db
 # Tests (development only)
 tests/
 
-# Exception: Allow colocated tests within integrations/graphiti
-!integrations/graphiti/tests/
-
 # Auto Claude data directory
 .auto-claude/
-coverage.json
+/gitlab-integration-tests/