diff --git a/scripts/doctor.sh b/scripts/doctor.sh
index 9f64bde..feaffd1 100644
--- a/scripts/doctor.sh
+++ b/scripts/doctor.sh
@@ -1,6 +1,7 @@
 #!/usr/bin/env bash
 # Read-only diagnostic checks for BAR-Devtools.
 # Expects: DEVTOOLS_DIR, COMPOSE, REPOS_CONF, REPOS_LOCAL (exported by Justfile)
+# source common.sh, repos.sh, and setup.sh first.
 
 pass_count=0
 warn_count=0
@@ -113,65 +114,31 @@ check_doctor_flatpak() {
   install_mode="$(flatpak info info.beyondallreason.bar 2>/dev/null | sed -n 's/^Installation: //p')"
   _pass "$ver, info.beyondallreason.bar installed ($install_mode)"
 
-  # Flatpak data dir where devtools symlinks would sit
-  local flatpak_data_dir="$HOME/.var/app/info.beyondallreason.bar/data"
-  [ -d "$flatpak_data_dir" ] || {
+  # Use the same game-dir discovery as setup (handles XDG_DATA_HOME overrides)
+  local game_dir
+  game_dir="$(detect_game_dir 2>/dev/null)" || true
+  if [ -z "$game_dir" ]; then
     echo ""
     return
-  }
-
-  # Collect permitted filesystem paths from Flatpak permissions (merged).
-  # Extract the line: filesystems=path:flag;path;path:ro;...
-  # then split on semicolons and strip trailing access-mode flags (:create, :ro, etc).
-  local -a permitted=("$flatpak_data_dir")
-  local perms_line
-  perms_line="$(flatpak info --show-permissions info.beyondallreason.bar 2>/dev/null | sed -n 's/^filesystems=//p')"
-  if [ -n "$perms_line" ]; then
-    local IFS=';'
-    local -a entries=($perms_line)
-    local e stripped
-    for e in "${entries[@]}"; do
-      [ -z "$e" ] && continue
-      # Strip access-mode flag after trailing colon
-      stripped="${e%:*}"
-      # Resolve tilde for ~/ paths and store as-is for absolute paths
-      case "$stripped" in
-        "~"/*) stripped="$HOME/${stripped#~/}" ;;
-        "~")   stripped="$HOME" ;;
-      esac
-      permitted+=("$stripped")
-    done
   fi
 
-  # Check each devtools symlink: is its target inside a permitted path?
+  # report which symlinks may be affected
+  # we have not yet checked permssions yet
   local linked_outside=0
   local -A link_map=(
-    [bar]="$flatpak_data_dir/games/Beyond-All-Reason.sdd"
-    [chobby]="$flatpak_data_dir/games/BYAR-Chobby.sdd"
-    [engine]="$flatpak_data_dir/engine/local-build"
+    [bar]="$game_dir/games/Beyond-All-Reason.sdd"
+    [chobby]="$game_dir/games/BYAR-Chobby.sdd"
+    [engine]="$game_dir/engine/local-build"
   )
-  local name link_path target perm
+  local name link_path target
   for name in bar chobby engine; do
     link_path="${link_map[$name]}"
     [ -L "$link_path" ] || continue
 
     target="$(readlink "$link_path")"
 
-    # No warning needed if the symlink target is in a flatpak-permitted path
-    local covered=0
-    for perm in "${permitted[@]}"; do
-      case "$target" in
-        "$perm"/*|"$perm")
-          covered=1
-          break
-          ;;
-      esac
-    done
-
-    [ "$covered" -eq 1 ] && continue
-
     if [ "$linked_outside" -eq 0 ]; then
-      _warn "$name symlink target is outside Flatpak sandbox"
+      info "$name symlink target is outside Flatpak sandbox"
       info "  $link_path -> $target"
       linked_outside=1
     else
@@ -180,9 +147,20 @@ check_doctor_flatpak() {
   done
 
   if [ "$linked_outside" -gt 0 ]; then
+    # If the flatpak already has access to DEVTOOLS_DIR, nothing to warn about.
+    # System installs need sudo to read overrides; warn the user first.
+    if [ "$install_mode" = "system" ]; then
+        info "  Checking system Flatpak permissions (may prompt for sudo)..."
+    fi
+    if flatpak_can_access_devtools_dir; then
+        echo ""
+        return
+    fi
+
     echo ""
-    warn "The Flatpak sandbox blocks the Spring engine from following symlinks"
-    warn "into folders it hasn't been granted access to."
+    _warn "The Flatpak sandbox blocks the Spring engine from following symlinks"
+    warn "into folders it hasn't been granted access to. "
+    warn "See above for symlinks targets currently outside that sandbox. "
     warn "Please grant access to these folders with:"
     if [ "$install_mode" = "system" ]; then
       warn "  sudo flatpak override info.beyondallreason.bar --filesystem=$DEVTOOLS_DIR"
@@ -194,6 +172,33 @@ check_doctor_flatpak() {
   echo ""
 }
 
+game_dir_has_engine() {
+  local dir="$1"
+  [ -d "$dir/engine" ] || return 1
+  local v
+  for v in "$dir"/engine/recoil_*; do
+    [ -d "$v" ] && return 0
+  done
+  return 1
+}
+
+check_doctor_game_dir() {
+  local game_dir
+  game_dir="$(detect_game_dir 2>/dev/null)" || true
+  if [ -z "$game_dir" ]; then
+    warn "Game directory not found. Set BAR_DATA_DIR env var in the .env file"
+    echo ""
+    return 0
+  fi
+  if game_dir_has_engine "$game_dir"; then
+    _pass "game directory exists and has engine"
+  else
+    _warn "game directory $game_dir has no engine folder or engine folder is empty."
+    echo "        This suggests BAR has never run from this folder."
+    echo "        Launch BAR once so the first-time downloader fetches the engine, then re-run 'just doctor'."
+  fi
+  echo ""
+}
 
 check_doctor_ports() {
   echo -e "${BOLD}Ports${NC}"
@@ -409,6 +414,7 @@ cmd_doctor() {
   check_doctor_env
   check_doctor_wsl
   check_doctor_flatpak
+  check_doctor_game_dir
   check_doctor_modules
   check_doctor_ports
   check_doctor_repos