Improve GenerateEverything

[MatthewDaggitt]

Instead of hard coding lists of modules that use certain flags, read the files themselves and detecting the flags.

[gallais]

Hard-coding the list means that if we forget to set the right options then we get told off.
This helps ensure we do respect the invariants.

If we're happily inferring the file's status from its options, then we lose this benefit.

[jamesmckinna]

I got caught by this today though, (adding a file and failing to update the hard-coded lists) and it took me a while to figure out the source of the problem.