Sometimes there comes situations where you want to add configuration to version control but they change depending on where you've cloned the project. How to "semi-ignore" these files depends totally on how you want it to work. So here are some strategies for it:
Strategy No. 1: Commit ALL THE THINGS
You should try to commit everything and see later on what you don't need. Sometimes this is the best solution. It is more common for us to assume that we don't need them in version control until we realize that we do.
You can also follow it up with temporarily assuming files as unchanged in git. The command you can use to do this with is
git update-index --assume-unchanged [file ...]
If you have trouble doing this with directories, read this SO question on assuming directories with untracked files.
Strategy No. 2: If a tool sets up the project, use it to generate the configuration and then clone on top of that
You can do what you've done now, ignore the configuration in git and when you want to clone the project you do that on top of a new project that is created by the tool. Or write your own tool (a batch script) to set up the project for you.
Strategy No. 3: Check in "default" configuration shared between projects
You could try to figure out which configuration is the bare minimum that you need and have that committed to the repository.
If you want configuration defaults, you could copy (or zip) all the configuration files to a seperate directory and then have that committed. When you clone, you can then unzip all those files to the correct spot to get things going.
You can batch this installation process to make it easier for you to get going. So that you only need to run it once when you clone the project.
Bonus Strategy: Check in a "readme" text file that details a process of how to get started
Checking in a text file that details how you go about to set up the project is a useful thing to do. You may need this later on to remind yourself how you've set up the project.