The most convenient way for distribution of internal apps for a particular organization is Apple Developer Enterprise Program, which allows installing apps directly from web.
In pre-iOS 9 ages it was sufficient to confirm that you trust XYZ Ltd. developer and installation took place. In iOS 9 it has become a little more complicated.
When trying to install an enterprise app, you get this error message:
|Untrusted Enterprise Developer|
|“iPhone Distribution: XYZ Ltd.” has not been trusted on this iPhone. Until this developer has been trusted their enterprise apps will not be available for use.|
As you can see, this error message is not very helpful. Luckily the solution is very simple. Go to:
Settings -> General -> Profile -> XYZ Ltd. -> Trust “XYZ Ltd.”
Now you can install any app form XYZ Ltd. developer.