To explain better:
I have a netbeans project that uploads files to my remote development server.
The project I'm working on was perfect for open source, so I created a new github repo. There were a lot of configuration files and other tidbits (like .htaccess files, etc.) that I did not want to include in the repo, so I just copied the files that I wanted into a new directory, created a git repo there, and I've been using that to push files to github.
Whenever I complete some new development in netbeans, I have to copy the new or edited files to the repo directory, commit the changes, and finally push to github.
I realize now that I can use a .gitignore file (git is new to me!). So I think it would be wise/faster to ignore the troublesome files and commit changes from the same directory I'm working in, thus eliminating the need to copy to the other directory. I assume that means I need to clone the repository into the directory I use for netbeans, but git tells me "that directory already exists."
How do I go about accomplishing what I need?