[ianopolous]

IPFS clearly does a lot more than storing and fetching files. Seriously, go have a read. A single hash can represent an arbitrarily large subtree of data (Microsoft's entire repo). Using an IPLD selector (in its simplest form, a path beyond the hash) an arbitrary sub component can be addressed. This can be used to avoid scanning entire subtrees (maintaining your O(changed files)). To commit your modifications is O(changed files + tree depth to the root of your modifications) you never need to do anything with the rest of the repo.

For tracking changes (i.e. mutable data) you can use IPNS and create a signed commit history. This will be built on IPFS eventually so it's only a matter of time.