[chj]

I know little about trust computing, but here's a thought.

To know whether an open source program on server is modified, we send a customized different executable copy every time with one time use secrets. So when the program starts, it has to answer questions correctly and shortly (to protect against reverse engineering) to prove it's a genuine copy, then we can send it our encrypted access key. The access key will never be written to disk by a genuine copy, so a restarted program won't be able to access our data without asking for a key again, then we will know something is wrong.

The copies we upload to server functions exactly like open source one, but the user is responsible for adding secret parts to it so that it's closed source.