We have a Visual Studio extension, currently installed with MSI, since we need to perform certain tasks after the installation (ngen, registering certain COM servers, etc). In t
The supported way to do it is with devenv /setup. You should use devenv /setup. I agree that it's somewhat slow an annoying, but it should work fine.
For your #2 point above, I would not use a single instance of a single issue reported by a single customer to indicate that it "may cause extensions not to load". Looking at that forum thread, the problem was never root-caused and so the actual problem can't be inferred.
For #1, yes, you can include additional files in a .vsix. Selecting files within Solution Explorer will show a "Include in VSIX" item in the properties window for that file. The main limitation is you can't control where the extension is, as a whole, installed. So you can happily make folders of stuff, as long as you're OK that it's still put under a randomly-named folder to begin with.