Managing the files and scripts on every site is tricky. Storing testing scripts, test sites, improper definitions in robots.txt and incorrect directory permission may create security vulnerability to your website. For good website management, one must follow these rules:
Never use your webspace as storage. Consider this as the first rule in website management. Always keep your website clean. Only keep files and scripts that are needed. Remember, if you keep any unnecessary script on your website it can be detected by some search engines and if it has a security vulnerability, it makes your whole website vulnerable.
If you want to test your scripts, use htaccess tools to password protect the directory where you are storing your test scripts/site.