Add note to docs about htaccess file when upgrading 3.0 to 3.1

Upgrade 3.0 to 3.1 docs should mention when copying the contents of the full package, that the htaccess file needs to be included (it is invisible in some OS's) and users have already begun updating to 3.1 w/o it and reporting issues with url rewrites not working for them, as a result.