Added external/pyflakes from https://github.com/kevinw/pyflakes.git
Add marmalade repo support. Replace pymacs and rope with jedi.

Signed-off-by: Sydney Weidman <sydney.weidman@gmail.com>
Added some installation notes.
Added require statement to init.el so that org support would be loaded early
Switched from python-mode to python.el; removed some ipython
configuration which was causing an error.
Moved electric pair config to run later in startup
Adding org-clock-persist, remove validation from export, set capture notes file
Removed submodules no longer being used
Removing submodules entirely