Pathogen not loading plugins correctly in Cygwin?

I recently discovered how awesome Pathogen is for managing Vim plugins, using the Git submodule approach for keeping plugins up-to-date with Github. You can view my modest dotfiles repo here.

I recently was forced to switch to a Windows development environment from for work, so the first thing I did was a complete install of Cygwin (I had hard drive space to spare and didn开发者_开发问答't feel like picking and chosing packages).

The problem: With Cygwin installed (using Mintty), I clone my dotfiles repo to ~/. Then I put symlinks in ~/ for .vim, .vimrc, and .bashrc. The .vimrc configuration file is being read in (the options work), but Pathogen isn't correctly loading my Vim plugins.

Forgive my incompetence, but I'm new to Cygwin and I don't fully understand its quirks yet. In any case, the exact same repository works fine under *nix machines. Is there something that I should be doing differently to get it to work under Cygwin?

Ok so I'm an idiot. I didn't realize that you have to do git submodule init and git submodule update after forking the repository as well (I thought you only had to do it on creation / first commit. To be clear, the issue had nothing to do with Cygwin specifically.

Which brings me to my next problem:
$ git submodule update
Cloning into .vim/bundle/nerdcommenter... error: SSL certificate problem, verify that the CA cert is OK. Details: error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed while accessing https://github.com/scrooloose/nerdcommenter.git/info/refs

fatal: HTTP request failed Clone of 'https://github.com/scrooloose/nerdcommenter.git' into submodule path '.vim/bundle/nerdcommenter' failed

Is there an quivalent of --no-check-certificate for wget?

Update: I fixed the latter problem as well. For anyone else having the same problem, you can simply edit your .git/config file and change all of the submodule HTTPS references to HTTP. Re-attempt the update and it should work.