Look through thermofluids running example and check for consistency

[Richard Murray]

There are now several thermofluids examples in the text. We need to look through the running example and make sure that we are using consistent notation, parameters, etc.

[Richard Murray]

Sent to Karl on 24 Jul. He will take a look and send back comments.

[Richard Murray]

Karl's updates in commit 04c7bb1 and b90472a, RMM updates in e6bd94f, 02d9d7d, 0d613c2.