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I don't quite understand the question. I suppose you have two sitefinity web applications in the solution but Thunder do not support that. Your solution must have only one sitefinity web application in it. Can you describe in detail what is happening and what's the problem?
Currently Thunder don't support more then one sitefinity web application in the solution because this is not а common scenario. We have it in mind. As for the other issues you have, right now Thunder only works if there are config files in \App_Data\Sitefinity\Configuration folder. Currently if those files are readonly you will get an error. We are aware of this problem. Everything that Thunder is doing "without ASKING" is by design. The idea is to do all the things for you without bothering, but if you have a custom flow of development this won't work. Тhank you for the feedback. We will consider all the comments on this.
Like I said right now thunder don't support such a custom project infrastructure. We have these thing in our checklist. I can't tell you exactly when but be sure that we will support this!