diff --git a/scripts/backup-appfactory.sh b/scripts/backup-appfactory.sh
index d1f68a0..258159d 100755
--- a/scripts/backup-appfactory.sh
+++ b/scripts/backup-appfactory.sh
@@ -1,22 +1,28 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-BASE_DIR="/opt/appfactory"
-BACKUP_DIR="$BASE_DIR/backups"
+CONFIG_FILE="/opt/appfactory/config/appfactory.env"
+source "$CONFIG_FILE"
+
 TIMESTAMP="$(date +%Y%m%d-%H%M%S)"
 BACKUP_FILE="$BACKUP_DIR/appfactory-backup-$TIMESTAMP.tar.gz"
 
 mkdir -p "$BACKUP_DIR"
 
-tar -czf "$BACKUP_FILE" \
-  /opt/appfactory/apps \
-  /opt/appfactory/config \
-  /opt/appfactory/data/gitea \
-  /opt/appfactory/data/registry \
-  /opt/appfactory/deploy \
-  /opt/appfactory/gateway \
-  /opt/appfactory/templates \
-  /opt/appfactory/services \
-  /home/jiri/workspace
-
+echo "Creating backup:"
+echo "$BACKUP_FILE"
+
+tar -czf "$BACKUP_FILE" \
+  "$APPFACTORY_DIR/apps" \
+  "$APPFACTORY_DIR/config" \
+  "$APPFACTORY_DIR/data/gitea" \
+  "$APPFACTORY_DIR/data/registry" \
+  "$APPFACTORY_DIR/deploy" \
+  "$APPFACTORY_DIR/gateway" \
+  "$APPFACTORY_DIR/templates" \
+  "$APPFACTORY_DIR/services" \
+  "$WORKSPACE_DIR"
+
+echo ""
+echo "DONE"
 echo "$BACKUP_FILE"
diff --git a/scripts/bootstrap-new-server.sh b/scripts/bootstrap-new-server.sh
index f77d9f4..85bff22 100755
--- a/scripts/bootstrap-new-server.sh
+++ b/scripts/bootstrap-new-server.sh
@@ -10,7 +10,6 @@ WORKSPACE_DIR="/home/$APP_USER/workspace"
 echo "======================================================"
 echo "AppFactory Bootstrap"
 echo "======================================================"
-echo ""
 echo "User:        $APP_USER"
 echo "Workspace:   $WORKSPACE_DIR"
 echo "AppFactory:  $APPFACTORY_DIR"
@@ -23,74 +22,30 @@ if [ "$CONFIRM" != "yes" ]; then
   exit 1
 fi
 
-echo ""
-echo "Updating system..."
-
 apt update
-apt install -y \
-  docker.io \
-  docker-compose-plugin \
-  git \
-  curl \
-  jq \
-  python3 \
-  python3-pip
-
-echo ""
-echo "Enabling Docker..."
+apt install -y docker.io docker-compose-plugin git curl jq python3 python3-pip
 
 systemctl enable docker
 systemctl start docker
 
-echo ""
-echo "Adding user to docker group..."
-
 usermod -aG docker "$APP_USER"
 
-echo ""
-echo "Creating directories..."
-
-mkdir -p "$APPFACTORY_DIR"
-mkdir -p "$APPFACTORY_DIR/apps"
-mkdir -p "$APPFACTORY_DIR/backups"
-mkdir -p "$APPFACTORY_DIR/config"
-mkdir -p "$APPFACTORY_DIR/data"
-mkdir -p "$APPFACTORY_DIR/data/gitea"
-mkdir -p "$APPFACTORY_DIR/data/registry"
-mkdir -p "$APPFACTORY_DIR/deploy"
-mkdir -p "$APPFACTORY_DIR/gateway"
-mkdir -p "$APPFACTORY_DIR/gateway/static"
-mkdir -p "$APPFACTORY_DIR/services"
-mkdir -p "$APPFACTORY_DIR/templates"
-
+mkdir -p "$APPFACTORY_DIR"/{apps,backups,config,data/gitea,data/registry,deploy,gateway/static,services,templates}
 mkdir -p "$WORKSPACE_DIR"
 
-echo ""
-echo "Creating config..."
-
-cat > "$APPFACTORY_DIR/config/appfactory.env" <<EOF
+cat > "$APPFACTORY_DIR/config/appfactory.env" <<EOF_ENV
 APP_USER="$APP_USER"
 APP_GROUP="$APP_GROUP"
 APPFACTORY_DIR="$APPFACTORY_DIR"
 WORKSPACE_DIR="$WORKSPACE_DIR"
 BACKUP_DIR="$APPFACTORY_DIR/backups"
-EOF
+EOF_ENV
 
 chmod 600 "$APPFACTORY_DIR/config/appfactory.env"
 
-echo ""
-echo "Fixing ownership..."
-
 chown -R "$APP_USER:$APP_GROUP" "$APPFACTORY_DIR"
 chown -R "$APP_USER:$APP_GROUP" "$WORKSPACE_DIR"
 
 echo ""
 echo "Bootstrap complete."
-echo ""
-echo "IMPORTANT:"
 echo "Logout/login again so docker group is applied."
-echo ""
-echo "Next steps:"
-echo "1. clone appfactory-tools"
-echo "2. restore backup"
-echo ""
diff --git a/scripts/delete-app.sh b/scripts/delete-app.sh
index b4dd337..d39874a 100755
--- a/scripts/delete-app.sh
+++ b/scripts/delete-app.sh
@@ -4,35 +4,24 @@ set -euo pipefail
 APP_ID="${1:-}"
 
 if [ -z "$APP_ID" ]; then
-  echo "Usage:"
-  echo "  ./delete-app.sh <app-id>"
+  echo "Usage: ./delete-app.sh <app-id>"
   exit 1
 fi
 
 CONFIG_FILE="/opt/appfactory/config/appfactory.env"
-
-if [ -f "$CONFIG_FILE" ]; then
-  source "$CONFIG_FILE"
-fi
-
-APPFACTORY_DIR="${APPFACTORY_DIR:-/opt/appfactory}"
-WORKSPACE_DIR="${WORKSPACE_DIR:-/home/jiri/workspace}"
+source "$CONFIG_FILE"
 
 COMPOSE_FILE="$APPFACTORY_DIR/deploy/apps-compose.yml"
 CATALOG_FILE="$APPFACTORY_DIR/apps/catalog.yml"
 CADDY_FILE="$APPFACTORY_DIR/gateway/Caddyfile"
-
 TOOLS_DIR="$WORKSPACE_DIR/appfactory-tools"
 
 echo "Deleting app: $APP_ID"
 
-if [ -n "${GITEA_URL:-}" ] && [ -n "${GITEA_TOKEN:-}" ] && [ -n "${GITEA_ORG:-}" ]; then
-  echo "Deleting Gitea repository..."
-
-  curl -sS -X DELETE \
-    "$GITEA_URL/api/v1/repos/$GITEA_ORG/$APP_ID" \
-    -H "Authorization: token $GITEA_TOKEN" || true
-fi
+echo "Deleting Gitea repository..."
+curl -sS -X DELETE \
+  "$GITEA_URL/api/v1/repos/$GITEA_ORG/$APP_ID" \
+  -H "Authorization: token $GITEA_TOKEN" || true
 
 echo "Stopping container..."
 docker rm -f "$APP_ID" || true
@@ -55,61 +44,37 @@ caddy_file = Path(sys.argv[4])
 def remove_block(lines, predicate):
     out = []
     i = 0
-
     while i < len(lines):
         line = lines[i]
-
         if predicate(line):
             indent = len(line) - len(line.lstrip())
             i += 1
-
             while i < len(lines):
                 next_line = lines[i]
-
                 if next_line.strip():
                     next_indent = len(next_line) - len(next_line.lstrip())
-
                     if next_indent <= indent:
                         break
-
                 i += 1
-
             continue
-
         out.append(line)
         i += 1
-
     return out
 
 if compose_file.exists():
-    compose_lines = compose_file.read_text().splitlines()
-
-    compose_lines = remove_block(
-        compose_lines,
-        lambda l: l.startswith(f"  {app_id}:")
-    )
-
-    compose_file.write_text("\n".join(compose_lines) + "\n")
+    lines = compose_file.read_text().splitlines()
+    lines = remove_block(lines, lambda l: l.startswith(f"  {app_id}:"))
+    compose_file.write_text("\n".join(lines).rstrip() + "\n")
 
 if catalog_file.exists():
-    catalog_lines = catalog_file.read_text().splitlines()
-
-    catalog_lines = remove_block(
-        catalog_lines,
-        lambda l: l.strip() == f"- id: {app_id}"
-    )
-
-    catalog_file.write_text("\n".join(catalog_lines) + "\n")
+    lines = catalog_file.read_text().splitlines()
+    lines = remove_block(lines, lambda l: l.strip() == f"- id: {app_id}")
+    catalog_file.write_text("\n".join(lines).rstrip() + "\n")
 
 if caddy_file.exists():
-    caddy_lines = caddy_file.read_text().splitlines()
-
-    caddy_lines = remove_block(
-        caddy_lines,
-        lambda l: f"/apps/{app_id}/*" in l
-    )
-
-    caddy_file.write_text("\n".join(caddy_lines) + "\n")
+    lines = caddy_file.read_text().splitlines()
+    lines = remove_block(lines, lambda l: f"/apps/{app_id}/*" in l)
+    caddy_file.write_text("\n".join(lines).rstrip() + "\n")
 PY
 
 echo "Regenerating generated files..."
diff --git a/scripts/deploy-app.sh b/scripts/deploy-app.sh
index d3e3c1c..5447773 100755
--- a/scripts/deploy-app.sh
+++ b/scripts/deploy-app.sh
@@ -4,19 +4,12 @@ set -euo pipefail
 APP_ID="${1:-}"
 
 if [ -z "$APP_ID" ]; then
-  echo "Usage:"
-  echo "  ./deploy-app.sh <app-id>"
+  echo "Usage: ./deploy-app.sh <app-id>"
   exit 1
 fi
 
 CONFIG_FILE="/opt/appfactory/config/appfactory.env"
-
-if [ -f "$CONFIG_FILE" ]; then
-  source "$CONFIG_FILE"
-fi
-
-APPFACTORY_DIR="${APPFACTORY_DIR:-/opt/appfactory}"
-WORKSPACE_DIR="${WORKSPACE_DIR:-/home/jiri/workspace}"
+source "$CONFIG_FILE"
 
 APP_SOURCE_DIR="$WORKSPACE_DIR/$APP_ID"
 CATALOG_FILE="$APPFACTORY_DIR/apps/catalog.yml"
@@ -32,14 +25,15 @@ if [ ! -f "$APP_SOURCE_DIR/Dockerfile" ]; then
   exit 1
 fi
 
+chown -R "$APP_USER:$APP_GROUP" "$APP_SOURCE_DIR" || true
+
 echo "Updating source code..."
 cd "$APP_SOURCE_DIR"
 
 if [ -d ".git" ]; then
+  git config --global --add safe.directory "$APP_SOURCE_DIR" || true
   git fetch origin main
   git reset --hard origin/main
-else
-  echo "WARNING: $APP_SOURCE_DIR is not a git repository"
 fi
 
 echo "Building Docker image..."
@@ -63,7 +57,7 @@ cat >> "$CATALOG_FILE" <<EOF_APP
 EOF_APP
 fi
 
-echo "Regenerating compose, Caddyfile and apps page..."
+echo "Regenerating generated files..."
 
 "$TOOLS_DIR/scripts/generate-apps-compose.sh"
 "$TOOLS_DIR/scripts/generate-caddyfile.sh"
@@ -77,4 +71,4 @@ docker compose -f docker-compose.yml -f apps-compose.yml up -d --force-recreate
 echo ""
 echo "DONE"
 echo "Open:"
-echo "${APPFACTORY_PUBLIC_URL:-http://192.168.66.130}/apps/$APP_ID/docs"
+echo "$APPFACTORY_PUBLIC_URL/apps/$APP_ID/docs"
diff --git a/scripts/generate-apps-compose.sh b/scripts/generate-apps-compose.sh
index 21066c5..5514b81 100755
--- a/scripts/generate-apps-compose.sh
+++ b/scripts/generate-apps-compose.sh
@@ -1,9 +1,11 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-BASE_DIR="/opt/appfactory"
-CATALOG_FILE="$BASE_DIR/apps/catalog.yml"
-COMPOSE_FILE="$BASE_DIR/deploy/apps-compose.yml"
+CONFIG_FILE="/opt/appfactory/config/appfactory.env"
+source "$CONFIG_FILE"
+
+CATALOG_FILE="$APPFACTORY_DIR/apps/catalog.yml"
+COMPOSE_FILE="$APPFACTORY_DIR/deploy/apps-compose.yml"
 
 cat > "$COMPOSE_FILE" <<'EOF_COMPOSE'
 services:
@@ -11,7 +13,6 @@ EOF_COMPOSE
 
 awk '
   /- id:/ { app=$3 }
-  /language:/ { lang=$2 }
   /status:/ {
     if (app != "") {
       print "  " app ":"
diff --git a/scripts/generate-apps-page.sh b/scripts/generate-apps-page.sh
index 6666242..f7b4462 100755
--- a/scripts/generate-apps-page.sh
+++ b/scripts/generate-apps-page.sh
@@ -1,14 +1,16 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-BASE_DIR="/opt/appfactory"
-CATALOG_FILE="$BASE_DIR/apps/catalog.yml"
-OUTPUT_DIR="$BASE_DIR/gateway/static"
+CONFIG_FILE="/opt/appfactory/config/appfactory.env"
+source "$CONFIG_FILE"
+
+CATALOG_FILE="$APPFACTORY_DIR/apps/catalog.yml"
+OUTPUT_DIR="$APPFACTORY_DIR/gateway/static"
 OUTPUT_FILE="$OUTPUT_DIR/apps.html"
 
 mkdir -p "$OUTPUT_DIR"
 
-cat > "$OUTPUT_FILE" <<'EOF'
+cat > "$OUTPUT_FILE" <<'EOF_HTML'
 <!doctype html>
 <html>
 <head>
@@ -31,7 +33,7 @@ cat > "$OUTPUT_FILE" <<'EOF'
   <th>Docs</th>
   <th>Health</th>
 </tr>
-EOF
+EOF_HTML
 
 awk '
   function print_row() {
@@ -57,10 +59,10 @@ awk '
   }
 ' "$CATALOG_FILE" >> "$OUTPUT_FILE"
 
-cat >> "$OUTPUT_FILE" <<'EOF'
+cat >> "$OUTPUT_FILE" <<'EOF_HTML'
 </table>
 </body>
 </html>
-EOF
+EOF_HTML
 
 echo "Generated: $OUTPUT_FILE"
diff --git a/scripts/generate-caddyfile.sh b/scripts/generate-caddyfile.sh
index e534345..1382f0d 100755
--- a/scripts/generate-caddyfile.sh
+++ b/scripts/generate-caddyfile.sh
@@ -1,9 +1,11 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-BASE_DIR="/opt/appfactory"
-CATALOG_FILE="$BASE_DIR/apps/catalog.yml"
-CADDY_FILE="$BASE_DIR/gateway/Caddyfile"
+CONFIG_FILE="/opt/appfactory/config/appfactory.env"
+source "$CONFIG_FILE"
+
+CATALOG_FILE="$APPFACTORY_DIR/apps/catalog.yml"
+CADDY_FILE="$APPFACTORY_DIR/gateway/Caddyfile"
 
 cat > "$CADDY_FILE" <<'EOF_CADDY'
 :80 {
@@ -48,4 +50,4 @@ cat >> "$CADDY_FILE" <<'EOF_CADDY'
 }
 EOF_CADDY
 
-docker exec appfactory-caddy caddy reload --config /etc/caddy/Caddyfile
+docker exec appfactory-caddy caddy reload --config /etc/caddy/Caddyfile || docker restart appfactory-caddy
diff --git a/scripts/new-python-app.sh b/scripts/new-python-app.sh
index 85d5595..4fbea82 100755
--- a/scripts/new-python-app.sh
+++ b/scripts/new-python-app.sh
@@ -1,24 +1,14 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-CONFIG_FILE="$HOME/.appfactory/env"
-
-if [ ! -f "$CONFIG_FILE" ]; then
-  echo "Missing config file: $CONFIG_FILE"
-  exit 1
-fi
-
+CONFIG_FILE="/opt/appfactory/config/appfactory.env"
 source "$CONFIG_FILE"
 
 APP_ID="${1:-}"
 APP_NAME="${2:-$APP_ID}"
 
 if [ -z "$APP_ID" ]; then
-  echo "Usage:"
-  echo "  ./new-python-app.sh <app-id> [app-name]"
-  echo ""
-  echo "Example:"
-  echo "  ./new-python-app.sh gmail-app \"Gmail App\""
+  echo "Usage: ./new-python-app.sh <app-id> [app-name]"
   exit 1
 fi
 
@@ -48,7 +38,7 @@ id: $APP_ID
 name: $APP_NAME
 language: python
 version: 1.0.0
-base_path: /$APP_ID
+base_path: /apps/$APP_ID
 port: 8000
 status: development
 EOF_APP
@@ -57,19 +47,6 @@ cat > README.md <<EOF_README
 # $APP_NAME
 
 Generated by AppFactory.
-
-## Local build
-
-\`\`\`bash
-docker build -t $APP_ID .
-docker run --rm -p 8001:8000 $APP_ID
-\`\`\`
-
-Open:
-
-\`\`\`text
-http://SERVER_IP:8001/docs
-\`\`\`
 EOF_README
 
 echo "Creating Gitea repository..."
@@ -122,6 +99,8 @@ git add .
 git commit -m "Initial $APP_NAME"
 git push -u origin main
 
+chown -R "$APP_USER:$APP_GROUP" "$TARGET_DIR" || true
+
 echo ""
 echo "DONE"
 echo "Repository:"
diff --git a/scripts/restore-appfactory.sh b/scripts/restore-appfactory.sh
index a8be496..3b99092 100755
--- a/scripts/restore-appfactory.sh
+++ b/scripts/restore-appfactory.sh
@@ -23,15 +23,6 @@ fi
 if [ "$FORCE" != "true" ]; then
   echo "REFUSING TO RUN RESTORE."
   echo ""
-  echo "Restore overwrites:"
-  echo "- $APPFACTORY_DIR"
-  echo "- $WORKSPACE_DIR"
-  echo "- Gitea data"
-  echo "- Registry data"
-  echo "- deployed apps"
-  echo "- catalog"
-  echo "- gateway config"
-  echo ""
   echo "Usage:"
   echo "  sudo ./restore-appfactory.sh --force /path/to/backup.tar.gz"
   exit 1
@@ -39,14 +30,11 @@ fi
 
 if [ -z "$BACKUP_FILE" ]; then
   echo "Missing backup file."
-  echo "Usage:"
-  echo "  sudo ./restore-appfactory.sh --force /path/to/backup.tar.gz"
   exit 1
 fi
 
 if [ ! -f "$BACKUP_FILE" ]; then
-  echo "Backup file not found:"
-  echo "$BACKUP_FILE"
+  echo "Backup file not found: $BACKUP_FILE"
   exit 1
 fi
 
@@ -61,8 +49,6 @@ echo "This will overwrite:"
 echo "  $APPFACTORY_DIR"
 echo "  $WORKSPACE_DIR"
 echo ""
-echo "Before restore, an emergency backup will be created."
-echo ""
 
 read -r -p "Type RESTORE to continue: " CONFIRM
 
@@ -72,29 +58,17 @@ if [ "$CONFIRM" != "RESTORE" ]; then
 fi
 
 TIMESTAMP="$(date +%Y%m%d-%H%M%S)"
-EMERGENCY_BACKUP_DIR="${BACKUP_DIR:-/opt/appfactory/backups}"
-EMERGENCY_BACKUP_FILE="$EMERGENCY_BACKUP_DIR/emergency-before-restore-$TIMESTAMP.tar.gz"
+EMERGENCY_BACKUP_FILE="$BACKUP_DIR/emergency-before-restore-$TIMESTAMP.tar.gz"
 
-mkdir -p "$EMERGENCY_BACKUP_DIR"
+mkdir -p "$BACKUP_DIR"
 
-echo ""
 echo "Creating emergency backup:"
 echo "$EMERGENCY_BACKUP_FILE"
 
 tar -czf "$EMERGENCY_BACKUP_FILE" \
   "$APPFACTORY_DIR" \
-  "$WORKSPACE_DIR" \
-  2>/tmp/appfactory-emergency-backup-errors.log || {
-    echo "Emergency backup failed."
-    echo "Errors:"
-    cat /tmp/appfactory-emergency-backup-errors.log
-    exit 1
-  }
+  "$WORKSPACE_DIR"
 
-echo ""
-echo "Emergency backup created."
-
-echo ""
 echo "Stopping AppFactory containers..."
 
 if [ -d "$APPFACTORY_DIR/deploy" ]; then
@@ -102,85 +76,41 @@ if [ -d "$APPFACTORY_DIR/deploy" ]; then
   docker compose -f docker-compose.yml -f apps-compose.yml down || true
 fi
 
-echo ""
-echo "Restoring files from backup..."
-
+echo "Restoring backup..."
 tar -xzf "$BACKUP_FILE" -C /
 
-echo ""
 echo "Fixing ownership..."
-
 chown -R "$APP_USER:$APP_GROUP" "$APPFACTORY_DIR"
 chown -R "$APP_USER:$APP_GROUP" "$WORKSPACE_DIR"
+chmod 600 "$APPFACTORY_DIR/config/appfactory.env" || true
 
-if [ -f "$APPFACTORY_DIR/config/appfactory.env" ]; then
-  chmod 600 "$APPFACTORY_DIR/config/appfactory.env"
-fi
-
-echo ""
 echo "Starting core services..."
-
 cd "$APPFACTORY_DIR/deploy"
-
 docker compose -f docker-compose.yml up -d
 
-echo ""
-echo "Regenerating generated files..."
-
 TOOLS_DIR="$WORKSPACE_DIR/appfactory-tools"
 
-if [ ! -d "$TOOLS_DIR" ]; then
-  echo "Missing tools directory:"
-  echo "$TOOLS_DIR"
-  echo ""
-  echo "Core services started, but app rebuild skipped."
-  exit 0
-fi
+if [ -d "$TOOLS_DIR" ]; then
+  cd "$TOOLS_DIR"
 
-cd "$TOOLS_DIR"
+  ./scripts/generate-apps-compose.sh || true
+  ./scripts/generate-caddyfile.sh || true
+  ./scripts/generate-apps-page.sh || true
 
-if [ -x "./scripts/generate-apps-compose.sh" ]; then
-  ./scripts/generate-apps-compose.sh
-fi
-
-if [ -x "./scripts/generate-caddyfile.sh" ]; then
-  ./scripts/generate-caddyfile.sh
-fi
-
-if [ -x "./scripts/generate-apps-page.sh" ]; then
-  ./scripts/generate-apps-page.sh
-fi
-
-echo ""
-echo "Rebuilding apps from workspace..."
-
-for app_dir in "$WORKSPACE_DIR"/*; do
-  if [ -f "$app_dir/app.yml" ]; then
-    app_id="$(basename "$app_dir")"
-
-    echo ""
-    echo "Rebuilding app: $app_id"
-
-    if [ -x "$TOOLS_DIR/scripts/deploy-app.sh" ]; then
-      "$TOOLS_DIR/scripts/deploy-app.sh" "$app_id" || {
-        echo "WARNING: failed to rebuild app: $app_id"
-      }
+  for app_dir in "$WORKSPACE_DIR"/*; do
+    if [ -f "$app_dir/app.yml" ]; then
+      app_id="$(basename "$app_dir")"
+      echo "Rebuilding app: $app_id"
+      ./scripts/deploy-app.sh "$app_id" || true
     fi
-  fi
-done
+  done
+fi
 
-echo ""
 echo "Final compose up..."
-
 cd "$APPFACTORY_DIR/deploy"
 docker compose -f docker-compose.yml -f apps-compose.yml up -d
 
 echo ""
 echo "DONE"
-echo ""
 echo "Emergency backup:"
 echo "$EMERGENCY_BACKUP_FILE"
-echo ""
-echo "Check:"
-echo "  docker ps"
-echo "  curl http://localhost/health"