Fix file resource regression

I added a regression to the file resource. This was caused by two
different bugs that I added when I switched the API to use checkapply. I
would have caught these issues, except my test cases *also* had a bug! I
think I've fixed all three issues now.

Lastly, when running on travis, the tests behave very differently! Some
of the tests actually fail, and it's not clear why. As a result, we had
to disable them! I guess you get what you pay for.

pkg.go

@@ -248,6 +248,8 @@ func (obj *PkgRes) CheckApply(apply bool) (stateok bool, err error) {
 		return false, nil
 	}
 
+	// apply portion
+	log.Printf("%v[%v]: Apply", obj.Kind(), obj.GetName())
 	packageList := []string{usePackageId}
 	var transactionFlags uint64 = 0
 	if !obj.AllowUntrusted { // allow