The colon : helps here, you can refer to the root of the repository by :/:
git init test
cd test
mkdir a
touch a/a
git add a
git commit -m a
# Here comes the interesting part:
cd a
touch ../root
git add :/
git commit -m root
The script above initializes a toy repository that contains one single file a in a subdirectory a. In "the interesting part", it changes to the a directory, creates an empty file in the root of the repository and adds it using the :/ reference. The -u switch works as usual (not shown in the script).
The manual of git-rev-parse reads:
<rev>:<path>, e.g. HEAD:README, :README, master:./README
A suffix : followed by a path names the blob or tree at the given path in the tree-ish object named by the part before the colon. :path (with an empty part before the colon) is a special case of the syntax described next: content recorded in the index at the given path. A path starting with ./ or ../ is relative to the current working directory. The given path will be converted to be relative to the working tree’s root directory. This is most useful to address a blob or tree from a commit or tree that has the same tree structure as the working tree.
Unfortunately, the bash autocompletion feature doesn't work for the :/ construct.
This related question asks about finding the absolute path of the repository; of course, you can also do git add $(git rev-parse --show-toplevel) as outlined in the top-voted answer.
