diff --git a/README.md b/README.md
index 4d56e98..c541c41 100644
--- a/README.md
+++ b/README.md
@@ -73,6 +73,14 @@ Prune migrated legacy backups from runtime folders (dry-run by default):
 ~/.mosaic/bin/mosaic-prune-legacy-runtime --runtime claude --apply
 ```
 
+Clean empty legacy runtime directories:
+
+```bash
+~/.mosaic/bin/mosaic-clean-runtime --runtime claude
+~/.mosaic/bin/mosaic-clean-runtime --runtime claude --apply
+~/.mosaic/bin/mosaic-clean-runtime --runtime claude --all-empty --apply
+```
+
 Audit runtime drift:
 
 ```bash
diff --git a/bin/mosaic-clean-runtime b/bin/mosaic-clean-runtime
new file mode 100755
index 0000000..dbacf48
--- /dev/null
+++ b/bin/mosaic-clean-runtime
@@ -0,0 +1,147 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+RUNTIME="claude"
+APPLY=0
+ALL_EMPTY=0
+
+usage() {
+  cat <<USAGE
+Usage: $(basename "$0") [options]
+
+Remove empty runtime directories created by migration/drift.
+Default mode only checks managed legacy surfaces. Use --all-empty for broader cleanup.
+
+Options:
+  --runtime <name>   Runtime to clean (default: claude)
+  --all-empty        Scan all runtime directories (except protected paths)
+  --apply            Perform deletions (default: dry-run)
+  -h, --help         Show help
+USAGE
+}
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    --runtime)
+      [[ $# -lt 2 ]] && { echo "Missing value for --runtime" >&2; exit 1; }
+      RUNTIME="$2"
+      shift 2
+      ;;
+    --all-empty)
+      ALL_EMPTY=1
+      shift
+      ;;
+    --apply)
+      APPLY=1
+      shift
+      ;;
+    -h|--help)
+      usage
+      exit 0
+      ;;
+    *)
+      echo "Unknown argument: $1" >&2
+      usage >&2
+      exit 1
+      ;;
+  esac
+done
+
+case "$RUNTIME" in
+  claude)
+    TARGET_ROOT="$HOME/.claude"
+    managed_roots=(
+      "$HOME/.claude/agent-guides"
+      "$HOME/.claude/scripts"
+      "$HOME/.claude/templates"
+      "$HOME/.claude/presets"
+      "$HOME/.claude/skills"
+      "$HOME/.claude/agents"
+      "$HOME/.claude/agents.bak"
+    )
+    protected_roots=(
+      "$HOME/.claude/.git"
+      "$HOME/.claude/debug"
+      "$HOME/.claude/file-history"
+      "$HOME/.claude/projects"
+      "$HOME/.claude/session-env"
+      "$HOME/.claude/tasks"
+      "$HOME/.claude/todos"
+      "$HOME/.claude/plugins"
+      "$HOME/.claude/statsig"
+      "$HOME/.claude/logs"
+      "$HOME/.claude/shell-snapshots"
+      "$HOME/.claude/paste-cache"
+      "$HOME/.claude/plans"
+      "$HOME/.claude/ide"
+      "$HOME/.claude/cache"
+    )
+    ;;
+  *)
+    echo "Unsupported runtime: $RUNTIME" >&2
+    exit 1
+    ;;
+esac
+
+[[ -d "$TARGET_ROOT" ]] || { echo "[mosaic-clean] Runtime dir missing: $TARGET_ROOT" >&2; exit 1; }
+
+is_protected() {
+  local path="$1"
+  for p in "${protected_roots[@]}"; do
+    [[ -e "$p" ]] || continue
+    case "$path" in
+      "$p"|"$p"/*)
+        return 0
+        ;;
+    esac
+  done
+  return 1
+}
+
+collect_empty_dirs() {
+  if [[ $ALL_EMPTY -eq 1 ]]; then
+    find "$TARGET_ROOT" -depth -type d -empty
+  else
+    for r in "${managed_roots[@]}"; do
+      [[ -d "$r" ]] || continue
+      find "$r" -depth -type d -empty
+    done
+  fi
+}
+
+count_candidates=0
+count_deletable=0
+
+while IFS= read -r d; do
+  [[ -n "$d" ]] || continue
+
+  count_candidates=$((count_candidates + 1))
+
+  # Never remove runtime root.
+  [[ "$d" == "$TARGET_ROOT" ]] && continue
+
+  if is_protected "$d"; then
+    continue
+  fi
+
+  count_deletable=$((count_deletable + 1))
+
+  if [[ $APPLY -eq 1 ]]; then
+    rmdir "$d" 2>/dev/null || true
+    if [[ ! -d "$d" ]]; then
+      echo "[mosaic-clean] deleted: $d"
+    fi
+  else
+    echo "[mosaic-clean] would delete: $d"
+  fi
+done < <(collect_empty_dirs | sort -u)
+
+mode="managed"
+[[ $ALL_EMPTY -eq 1 ]] && mode="all-empty"
+
+if [[ $APPLY -eq 1 ]]; then
+  echo "[mosaic-clean] complete: mode=$mode deleted_or_attempted=$count_deletable candidates=$count_candidates runtime=$RUNTIME"
+else
+  echo "[mosaic-clean] dry-run: mode=$mode deletable=$count_deletable candidates=$count_candidates runtime=$RUNTIME"
+  echo "[mosaic-clean] re-run with --apply to delete"
+fi