Failed Git Update after using this plugin.

[eangulus]

Not sure if to really call this a bug, but a solutions is needed.

I am currently developing a full WordPress site using Git. I submitted a commit after adding the Envato wp Toolkit. I then updated one of my themes (The Retailer).

I then spent hours and hours trying to work out why, the Retailer theme folder was refusing to get updated on Git. I thought it was a GitHub for Windows issue or something. Anyway after manually looking at the files in the folder, I saw .git files. Once I removed those, all went well.

Why are they there, is there a need to have them there, and is there a way we can have at least an option in the settings to not have them or to clean out any that are there?