Fix some machine-code theories for pat_assum rename

Add a theorem about fun2set.

Various minor changes.

Remove trailing whitespace in source files.

Minor tweaks.

Many minor additions/changes.

Minor update.

A general update.

Many minor updates.

Removed trailing whitespace from all .sml and .sig files.

This affects over 900 files and was done using emacs's delete-trailing-whitespace
function in batch mode. Building the system with Poly/ML and Moscow ML seems to
work, so I'm hoping these changes don't break anything. Please complain if
they do!

A general update:
1. the decompiler is now slightly faster, due to new code
abbreviations (terms smaller in internal proofs);
2. the definition of the machine-code Hoare triple
was slightly altered to support instruction caches;
3. the x86 model now includes an instruction cache.

Also, I give up on attempting to support MoscowML for
examples/machine-code/lisp. Both the standard kernel and the
experimental kernel crash while loading files in this
directory using the latest patched version of MoscowML.
Both kernels exit with an uninformative message:

Compiling lisp_equalScript.sml
Linking lisp_equalScript.uo to produce theory-builder executable
Uncaught exception: Chr
Failed to build script file, lisp_equalScript

Did they run out of memory? If so, why does the error message not
say so?

Restructuring and simplification.

A new version of files previously in examples/mc-logic.
Eventually examples/mc-logic will be deleted.