Update species representation documentation (adjlist update for O2)

A student pointed this out to me (since using this will of course cause
RMG to fail), just updating it now before I forget.
Remove unused CoreEdgeReactionModel.loadSeedMechanism() method.

I think this stopped being used four years ago in commit 3599f34b550ef7a53ad7081d62b93aa41c44e057
Author: Josh Allen <jwallen@mit.edu>
Date:   Thu Aug 5 15:32:43 2010 -0400
and is now thoroughly broken. Removing it to reduce confusion.
Add .gitignore to prevent output in rmgpy/cantherm/files being tracked.

These will only appear if you manually run cantherm on the input file,
as I don't think (currently) this is done as part of a unit test 
(though I don't see why it couldn't be in the future).
Refactor the pruning algorithm a little bit.

This should be a bit faster, and a bit clearer.
Faster because we have fewer lookups of self.edge.species[index]
and because we can stop iterating as soon as we reach a small enough edge.

Now that this has been debugged, I'm not sure we need the logging statement
on line 1101, because the same info is logged about 15 lines further down...
Add description to the methoxy example README (and rename README.txt)
Revert "Minor import fix in makeProfileGraph funciton."

This reverts commit ae84b9b3979329fb7e9745e844af1a0bcf1d6b44.

It was changed the other way in c881a72a8e442c6fb2672837c84100b325b069d5.
I suggest checking gprof2dot is not in your $RMGpy/external/ folder,
and that you have a recent version (eg. via `pip install --upgrade gprof2dot`)
Attempt to clarify #290 re. Symmetry corrections in HBI radical GA estimates.

I changed a method name, added an assertion, and added some text to the docstring.
Just trying to clarify what is currently being done, without changing anything.

My remaining concern is with how this interacts with QMThermo, where the "stable" 
(saturated parent) molecule is estimated via PM6 or something. This current 
implementation assumes that the the entropy has not been corrected for symmetry
(because that is what it now does for group additive thermo).