The developer at Microsoft who created the tool was doing it in his free time and we haven't had a response from him recently. Basically we got to the point where the latest of our code worked with the latest of his code except for one problem.
If you know about .NET licensing, a yourapp.exe.licenses file is embedded in the assembly which contains information generated from the licenses.licx file. It is some sort of hashtable that has entries for full type name and then the compiled license data. So what happens after the merge is that the full type names of the licensed controls has changed since instead of them being in an assembly like ActiproSoftware.SyntaxEditor.Net20.dll, they are now in MergedApp.exe.
So to review, the .licenses file still would have the full type name as "ActiproSoftware.SyntaxEditor.SyntaxEditor, ActiproSoftware.SyntaxEditor.Net20, ..." but now SyntaxEditor is in MergedApp.exe so when our licensing code asks .NET for a license for the SyntaxEditor Type, it is asking for a lookup on "ActiproSoftware.SyntaxEditor.SyntaxEditor, MergedApp, ..." but there is no entry for that key.
That is the remaining issue that I see. I'm not sure how to work around it from our end. Somehow the .licenses file needs to be updated so that the entries point to the new merged assembly instead of the pre-merged ones.
Make sense, anyone have any ideas?