diff --git a/.github/workflows/cd.yaml b/.github/workflows/cd.yaml
index 9caf0f1f..490c393b 100644
--- a/.github/workflows/cd.yaml
+++ b/.github/workflows/cd.yaml
@@ -103,7 +103,12 @@ jobs:
       api: ${{ inputs.force_deploy == true && 'true' || steps.filter.outputs.api }}
       web: ${{ inputs.force_deploy == true && 'true' || steps.filter.outputs.web }}
     steps:
+      - name: Clean worktrees
+        run: rm -rf .claude/worktrees 2>/dev/null || true
+
       - uses: actions/checkout@v4
+        with:
+          clean: true
 
       - uses: dorny/paths-filter@v3
         id: filter
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 9f29acc3..77151097 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -44,7 +44,12 @@ jobs:
     needs: pre-flight
     timeout-minutes: 10
     steps:
+      - name: Clean worktrees
+        run: rm -rf .claude/worktrees 2>/dev/null || true
+
       - uses: actions/checkout@v4
+        with:
+          clean: true
 
       - name: Setup pnpm
         uses: pnpm/action-setup@v3