What I did:
I think there were some weird configurations from the github gui that caused this issue and prevented me from being able to easily use git from command line or even git-bash.
I ended up just uninstalling github and git then reinstalling just git for windows. I now have everything running off the command line(except ssh which I run from git-bash). Much easier and more reliable that the github gui.
Thanks to mu 無 for taking the time to try to figure this out. I didn't end up using his answer, but if I hadn't needed to do a reinstall of git it would have been what I needed to do.
I am using the github gui on my local machine. I just noticed that a commit I was about to make was going to update all of my recently update node modules. I set up my .gitignore to ignore the entire node_modules/ directory.
I'm not sure what to do about this. All the file types I included in .gitignore were ignored. It's just the directories that it seems to ignore.
Here is my .gitignore file:
#################
## Sublime Text
#################
*.sublime-project
*.sublime-workspace
#################
## Images
#################
*.jpg
*.jpeg
*.png
*.gif
*.psd
*.ai
#################
## Windows detritus
#################
# Windows image file caches
Thumbs.db
ehthumbs.db
# Folder config file
Desktop.ini
# Recycle Bin used on file shares
$RECYCLE.BIN/
# Mac crap
.DS_Store
#################
## Directories
#################
dev/
cms/core/config/
node_modules/
Since the node_modules directory is already tracked as part of the repository, the .gitignore rule will not apply to it.
You need to untrack the directory from git using
git rm -r --cached node_modules
git commit -m "removing node_modules"
You can run the above 2 in git-bash.
After this, the .gitignore rule will ignore the directory away.
Note that this will remove the directory node_modules from your other repos once you pull the changes in. Only the original repo where you made that commit will still have the node_modules folder there.