Add basic "robots.txt" files to exclude system/php folders from Spidering/Indexing.
Folder will include:
Disallow: /admin/
Disallow: /core/
Disallow: /custom/
Disallow: /in-auction/
Disallow: /in-bulletin/
Disallow: /in-commerce/
Disallow: /in-link/
Disallow: /in-news/
Disallow: /system/
Disallow: /themes/
Disallow: /tools/