Hey Scott,
I would assume that running in https is no problem?
Correct, wyUpdate fully support HTTPS.
We would like to have everything except the release notes able to be handled through command line from the build server. Would this be an issue?
Nope, that's no problem. You can build updates from commandline.
The one problem I am thinking of is, we want the app to build release ready with the update site being our release site, but we want our testing team to be able to change the client.wyc file (I think?) to point to the staging server for the updates that were automatically built.
There are a few ways to do this. You can use either the -server or -updatepath commandline switches to accomplish that.
We have some clients with really tight IT restrictions and would need to be sent the dif file in an email and then update manually. Would this pose a problem? Telling the updater to look in a local folder?
Sure, you can do that. The -updatepath option is the way you want to go.
The initial install file that clients use to install the app will have to be build containing wybuild.exe and client.wyc correct?
Almost correct: wyUpdate.exe and the client.wyc.
So if in the future we want to upgrade from 1.9 to 2.0 and starting in 2.0 we want to switch the location of the updates server, can we include an updated client.wyc file with the update that took them from 1.0 to 2.0?
Yes.
My last question how could we identify what users get what update? Could we use a wcf service so in order to get to the updates the app must supply a user name and password?
We cover this topic here: How to prevent or limit updates.
If you have any other questions or need clarification we'll be glad to help.