In the case where one wants to create a tree commit derived from other content, using rofiles-fuse in concert with ostree commit --link-checkout-speedup (or the underlying API) can ensure that only new files are checksummed.
# Initialize a checkout and mount
$ ostree --repo=repo checkout somebranch branch-checkout
$ mkdir mnt
$ rofiles-fuse branch-checkout mnt
# Now, arbitrary changes to mnt/ are reflected in branch-checkout
$ echo somenewcontent > mnt/anewfile
$ mkdir mnt/anewdir
$ rm mnt/someoriginalcontent -rf
# Commit and cleanup
$ fusermount -u mnt
$ ostree --repo=repo commit --link-checkout-speedup -b somebranch -s 'Commit new content' --tree=dir=branch-checkout
$ rm mnt branch-checkout -rf
ostree(1)