How do I open / close the Combine gates or lock / unlock the normal doors?
The spawned doors behave exactly like map entities. In order to control them, you have to fire their inputs.
For combine gates: "setanimation" "open" / "setanimation" "close"
For rotating doors: "open" / "close" / "lock" / "unlock"
I strongly recommend you get my Entity:fire() function for Expression 2. Then you can control these doors via wire.
Other tools that can interact with doors: Sonic Screwdriver, Alyx EMP Swep, Extended Properties,...

Can you add Wire inputs / outputs to the doors?
Sorry, but no. If you want Wire inputs, you should get the Wire Doors STools from Wiremod's SVN. The purpose of this addons is to make the doors easily dupeable by recreating them each time via E2. You would have to renew the wires all the time which is not as comfortable as just firing the inputs.

Can I move the doors with the Physgun?
For the prop_dynamic doors: No, I disabled that, because it doesn't move the collision and f**** up the door. For the other doors: Yes, but do not rotate them, because if you do, they will no longer open correctly.

Can I use this in multiplayer?
If it's installed server-side, then yes. If you have a CPPI compatible Prop Protection addon, then the door's owner will register correctly to the player that spawned it. Otherwise it'll be owned by the world, which shouldn't be a problem, if you don't use Prop Protection.

Does this have any bugs / issues?
Yes, some small issues are there:
- The models spawn differently on the coordinates you provided. For example, the Combine gate no. 1 spawns 90° rotated, the gates 2 and 3 do not. Some spawn with their center at the position, others with their corners. I don't have the time to make spawning for each model individually. You will have to live with that.
- Most prop_dynamic doors don't have any sounds. I don't have the time to look for fitting sound files, but you can always play some sound using E2.
- If you spawn a rotating door where the E2 chip is (via entity():pos()), then you have to move or remove (put selfDestruct() in the code) the E2 chip or it'll block the door from closing again.

Please remember, that this was a personal project, that works fine for me and that I'm just sharing for those who might find it useful. If you can live with that, then please enjoy it.