elpy-refactor-insert-changes: Add argument CHANGES

This was not passed before, which only worked because Emacs Lisp is
dynamically scoped.
Bump version strings to 0.9, somehow that got missed in the release.
Fixes to remove some compilation warnings
elpy-doc: Use symbol at point with no prefix arg.

Adding double prefix arg support introduced a bug where this would
always ask for a symbol to be entered. With this commit, the
function should default to the symbol at point with no prefix arg
as before.

Fixes #61
elpy-enable: New optional argument, skip-initialize-variables

When this is a true value, Elpy will not call
`elpy-initialize-variables`, allowing the user to configure Elpy's
support modes themselves.

Fixes #59
README.md: Mention package-refresh-contents.

This needs to be called to load the data from the new repository.

Fixes #58
python-check.sh: Remove in favor of flake8

flake8 combines and improves pyflakes and pep8, so is strictly
better than python-check.sh, as we dropped pylint support a while
ago.

Fixes #57
flymake-warning-re: Set in buffer initialization function.

This is a buffer-local variable. Setting it in the variable
initialization function does not make all that much sense. Set
it in the buffer initialization function.