diff --git a/.claude/commands/issue/execute.md b/.claude/commands/issue/execute.md
index a7cda446..c31567b3 100644
--- a/.claude/commands/issue/execute.md
+++ b/.claude/commands/issue/execute.md
@@ -148,9 +148,14 @@ TodoWrite({
 
 console.log(`\n### Executing Solutions (DAG batch 1): ${batch.join(', ')}`);
 
-// Setup worktree base directory if needed
+// Setup worktree base directory if needed (using absolute paths)
 if (useWorktree) {
-  Bash('mkdir -p ../.worktrees');
+  // Use absolute paths to avoid issues when running from subdirectories
+  const repoRoot = Bash('git rev-parse --show-toplevel').trim();
+  const worktreeBase = `${repoRoot}/.ccw/worktrees`;
+  Bash(`mkdir -p "${worktreeBase}"`);
+  // Prune stale worktrees from previous interrupted executions
+  Bash('git worktree prune');
 }
 
 // Launch ALL solutions in batch in parallel (DAG guarantees no conflicts)
@@ -167,13 +172,34 @@ batch.forEach(id => updateTodo(id, 'completed'));
 
 ```javascript
 function dispatchExecutor(solutionId, executorType, useWorktree = false) {
-  // Worktree setup commands (if enabled)
+  // Worktree setup commands (if enabled) - using absolute paths
   const worktreeSetup = useWorktree ? `
 ### Step 0: Setup Isolated Worktree
 \`\`\`bash
+# Use absolute paths to avoid issues when running from subdirectories
+REPO_ROOT=$(git rev-parse --show-toplevel)
+WORKTREE_BASE="\${REPO_ROOT}/.ccw/worktrees"
 WORKTREE_NAME="exec-${solutionId}-$(date +%H%M%S)"
-WORKTREE_PATH="../.worktrees/\${WORKTREE_NAME}"
+WORKTREE_PATH="\${WORKTREE_BASE}/\${WORKTREE_NAME}"
+
+# Ensure worktree base exists
+mkdir -p "\${WORKTREE_BASE}"
+
+# Prune stale worktrees
+git worktree prune
+
+# Create worktree
 git worktree add "\${WORKTREE_PATH}" -b "\${WORKTREE_NAME}"
+
+# Setup cleanup trap for graceful failure handling
+cleanup_worktree() {
+  echo "Cleaning up worktree due to interruption..."
+  cd "\${REPO_ROOT}" 2>/dev/null || true
+  git worktree remove "\${WORKTREE_PATH}" --force 2>/dev/null || true
+  echo "Worktree removed. Branch '\${WORKTREE_NAME}' kept for inspection."
+}
+trap cleanup_worktree EXIT INT TERM
+
 cd "\${WORKTREE_PATH}"
 \`\`\`
 ` : '';
@@ -190,8 +216,8 @@ AskUserQuestion({
     header: "Merge",
     multiSelect: false,
     options: [
-      { label: "Merge to main", description: "Merge branch and cleanup worktree" },
-      { label: "Create PR", description: "Push branch and create pull request" },
+      { label: "Create PR (Recommended)", description: "Push branch and create pull request - safest for parallel execution" },
+      { label: "Merge to main", description: "Merge branch and cleanup worktree (requires clean main)" },
       { label: "Keep branch", description: "Cleanup worktree, keep branch for manual handling" }
     ]
   }]
@@ -200,22 +226,44 @@ AskUserQuestion({
 
 **Based on selection:**
 \`\`\`bash
-MAIN_REPO=$(git worktree list | head -1 | awk '{print $1}')
-cd "\${MAIN_REPO}"
+# Disable cleanup trap before intentional cleanup
+trap - EXIT INT TERM
 
-# Merge to main:
-git merge --no-ff "\${WORKTREE_NAME}" -m "Merge solution ${solutionId}"
-git worktree remove "\${WORKTREE_PATH}" && git branch -d "\${WORKTREE_NAME}"
+# Return to repo root (use REPO_ROOT from setup)
+cd "\${REPO_ROOT}"
 
-# Create PR:
+# Validate main repo state before merge
+validate_main_clean() {
+  if [[ -n \$(git status --porcelain) ]]; then
+    echo "⚠️ Warning: Main repo has uncommitted changes."
+    echo "Cannot auto-merge. Falling back to 'Create PR' option."
+    return 1
+  fi
+  return 0
+}
+
+# Create PR (Recommended for parallel execution):
 git push -u origin "\${WORKTREE_NAME}"
 gh pr create --title "Solution ${solutionId}" --body "Issue queue execution"
 git worktree remove "\${WORKTREE_PATH}"
 
+# Merge to main (only if main is clean):
+if validate_main_clean; then
+  git merge --no-ff "\${WORKTREE_NAME}" -m "Merge solution ${solutionId}"
+  git worktree remove "\${WORKTREE_PATH}" && git branch -d "\${WORKTREE_NAME}"
+else
+  # Fallback to PR if main is dirty
+  git push -u origin "\${WORKTREE_NAME}"
+  gh pr create --title "Solution ${solutionId}" --body "Issue queue execution (main had uncommitted changes)"
+  git worktree remove "\${WORKTREE_PATH}"
+fi
+
 # Keep branch:
 git worktree remove "\${WORKTREE_PATH}"
 echo "Branch \${WORKTREE_NAME} kept for manual handling"
 \`\`\`
+
+**Parallel Execution Safety**: "Create PR" is the default and safest option for parallel executors, avoiding merge race conditions.
 ` : '';
 
   const prompt = `
diff --git a/.codex/prompts/issue-execute.md b/.codex/prompts/issue-execute.md
index f329e72d..34470bd1 100644
--- a/.codex/prompts/issue-execute.md
+++ b/.codex/prompts/issue-execute.md
@@ -15,18 +15,40 @@ When `--worktree` is specified, create a separate git worktree to isolate work:
 
 ```bash
 # Step 0: Setup worktree before starting
+
+# Use absolute paths to avoid issues when running from subdirectories
+REPO_ROOT=$(git rev-parse --show-toplevel)
+WORKTREE_BASE="${REPO_ROOT}/.ccw/worktrees"
 WORKTREE_NAME="issue-exec-$(date +%Y%m%d-%H%M%S)"
-WORKTREE_PATH="../.worktrees/${WORKTREE_NAME}"
+WORKTREE_PATH="${WORKTREE_BASE}/${WORKTREE_NAME}"
+
+# Ensure worktree base directory exists (gitignored)
+mkdir -p "${WORKTREE_BASE}"
+
+# Prune stale worktrees from previous interrupted executions
+git worktree prune
 
 # Create worktree from current branch
 git worktree add "${WORKTREE_PATH}" -b "${WORKTREE_NAME}"
 
+# Setup cleanup trap for graceful failure handling
+cleanup_worktree() {
+  echo "Cleaning up worktree due to interruption..."
+  cd "${REPO_ROOT}" 2>/dev/null || true
+  git worktree remove "${WORKTREE_PATH}" --force 2>/dev/null || true
+  # Keep branch for debugging failed executions
+  echo "Worktree removed. Branch '${WORKTREE_NAME}' kept for inspection."
+}
+trap cleanup_worktree EXIT INT TERM
+
 # Change to worktree directory
 cd "${WORKTREE_PATH}"
 
 # Now execute in isolated worktree...
 ```
 
+**Note**: Add `.ccw/worktrees/` to `.gitignore` to prevent tracking worktree contents.
+
 **Benefits:**
 - Parallel executors don't conflict with each other
 - Main working directory stays clean
@@ -63,16 +85,35 @@ AskUserQuestion({
 **Based on user selection:**
 
 ```bash
-# Return to main repo first
-MAIN_REPO=$(git worktree list | head -1 | awk '{print $1}')
-cd "${MAIN_REPO}"
+# Disable cleanup trap before intentional cleanup
+trap - EXIT INT TERM
 
-# Option 1: Merge to main
-git merge "${WORKTREE_NAME}" --no-ff -m "Merge issue queue execution: ${WORKTREE_NAME}"
-git worktree remove "${WORKTREE_PATH}"
-git branch -d "${WORKTREE_NAME}"
+# Return to main repo first (use REPO_ROOT from setup)
+cd "${REPO_ROOT}"
 
-# Option 2: Create PR
+# Validate main repo state before merge (prevents conflicts)
+validate_main_clean() {
+  if [[ -n $(git status --porcelain) ]]; then
+    echo "⚠️ Warning: Main repo has uncommitted changes."
+    echo "Cannot auto-merge. Falling back to 'Create PR' option."
+    return 1
+  fi
+  return 0
+}
+
+# Option 1: Merge to main (only if main is clean)
+if validate_main_clean; then
+  git merge "${WORKTREE_NAME}" --no-ff -m "Merge issue queue execution: ${WORKTREE_NAME}"
+  git worktree remove "${WORKTREE_PATH}"
+  git branch -d "${WORKTREE_NAME}"
+else
+  # Fallback to PR if main is dirty
+  git push -u origin "${WORKTREE_NAME}"
+  gh pr create --title "Issue Queue: ${WORKTREE_NAME}" --body "Automated issue queue execution (main had uncommitted changes)"
+  git worktree remove "${WORKTREE_PATH}"
+fi
+
+# Option 2: Create PR (Recommended for parallel execution)
 git push -u origin "${WORKTREE_NAME}"
 gh pr create --title "Issue Queue: ${WORKTREE_NAME}" --body "Automated issue queue execution"
 git worktree remove "${WORKTREE_PATH}"
@@ -84,6 +125,8 @@ git worktree remove "${WORKTREE_PATH}"
 echo "Branch '${WORKTREE_NAME}' kept. Merge manually when ready."
 ```
 
+**Parallel Execution Safety**: For parallel executors, "Create PR" is the safest option as it avoids race conditions during merge. Multiple PRs can be reviewed and merged sequentially.
+
 ## Execution Flow
 
 ```