git add . has added the content of your files into git ; unfortunately, it hasn't created a 'directory' structure which lists your files with their names.
What you can do :
run
git fsck --full --unreachable --no-reflog | grep blob > blobs.txt
# the content of blobs.txt will look like :
unreachable blob 08bf360988858a012dab3af4e0b0ea5f370a2ae8
unreachable blob 21bf7ea93f9f9cc2b3ecbed0e5ed4fa45c75eb89
unreachable blob 08c12ef37075732cf4645269ab5687ba6ba68943
...
For each of these blobs, you can dump the content to disk :
cat blobs.txt | awk '{ print $3 }' | while read blobid; do
    git show $blobid > $blobid.txt
done
You will now have a list of files :
08bf360988858a012dab3af4e0b0ea5f370a2ae8.txt
21bf7ea93f9f9cc2b3ecbed0e5ed4fa45c75eb89.txt
08c12ef37075732cf4645269ab5687ba6ba68943.txt
...
The good news is : all the files that were present in the initial git add . should be represented in there.
The bad news is :
- this list will also contain the files you wanted to ignore initially (I assume you added your 
node_modules/ folder, so you would have the code for all the js libs you added ...) , 
- you will have to figure out what files went where, and rename them to 
src/my_controller.js, src/model/my_model.js ... 
One first filter you could apply, to try to take the node_modules/ files away is :
- in the list of blobs above, try to find your package.json file (
grep -e some_package_I_remember), 
- rename it to 
package.json (you may also find the lockfile), and run npm install or yarn install 
- this should create a 
node_modules/ folder, which looks a lot like the previous one you had 
- add that 
node_modules/ folder, and create a commit, 
- now, the blobs in node_modules are no longer unreachable ; re-run the 
git fsck ... > blobs.txt above, you should have a list of what wasn't under node_modules ...