Update comment on pinned web2py 2.8.2 and patches

These were originally together in the same file, but have become
separated. (This looks OK, since our web2py patches don't seem to be
needed for the phylesystem API.)
Reset patched rewrite.py to vanilla web2py 2.8.2

This is just for future reference, to clarify the changes we've made
to this and other web2py files. I'll restore our patch in the next
commit.
Show exact changes from web2py 2.8.2
Revert "Update comment on pinned web2py 2.8.2 and patches"

This reverts commit d7d316c8bab17d5db38df472206dd5ac6895d937.
Adding helpful comments to modified web2py files.

This should help future maintainers to make sense of our changes and
how/whether to apply them in later versions of web2py.
Adding summary of changes to web2py files.
Merge pull request #489 from OpenTreeOfLife/clarify-web2py-patches

Clarify web2py patches