Why does this rule not appear in the UI and how can I clone it?
I don't think it's possible to delete this Rule. Even if you delete it from the database directly, it is recreated the first time Commerce gets called (because it's in the defaults .inc file).
Are you sure it's not just disabled?
Your module directory structure is non-standard; Commerce should be in sites/all/modules/contrib.


Here's a copy of the Rule in case you need to import it again:

{ "commerce_checkout_order_email" : {
"LABEL" : "Send an order notification e-mail",
"PLUGIN" : "reaction rule",
"WEIGHT" : "4",
"OWNER" : "rules",
"TAGS" : [ "Commerce Checkout" ],
"REQUIRES" : [ "rules", "commerce_checkout" ],
"ON" : { "commerce_checkout_complete" : [  ] },
"DO" : [
  { "mail" : {
      "to" : [ "commerce-order:mail" ],
      "subject" : "Order [commerce-order:order-number] at [site:name]",
      "message" : "Thanks for your order [commerce-order:order-number] at [site:name].\u000A\u000AIf this is your first order with us, you will receive a separate e-mail with login instructions. You can view your order history with us at any time by logging into our website at:\u000A\u000A[site:login-url]\u000A\u000AYou can find the status of your current order at:\u000A\u000A[commerce-order:customer-url]\u000A\u000APlease contact us if you have any questions about your order.",
      "from" : ""
        }
      }
    ]
  }
}