Add plugins back and make Pathogen works.

Vundle does not handle non-Git-hosted repositories, so we still need
Pathogen again to handle plugins with Git submodules manually.

* Add Pathogen back and it handles plugins under bundle-pathogen now.
* Change the source of most of the plugins to the mirror of vim-scripts,
  and manage them with Vundle.
* Bypass all the changes under bundle folder to Vundle. Note: use
  ":BundleUpdate" to update them.
* Remove some plugins which is out of maintenance.