commitctx: create the `ChangingFiles` object sooner Let us change the `_commit_manifest` call before other changes.

commitctx: move ChangingFiles creation directly inside `_process_files` As announced, we move it there. We focus on the signature change first, we will update the code afterward.

commitctx: create the ChangingFiles object directly in the various case No need to compute all data then create the object, we can create it early and directly store data in it. We start simple by moving create higher in the function, but the end goal is to eventually move the creation inside the `_process_files` function to take advantage of the object there.

commitctx: no longer make the storage and added/removed file optional The code using this variable is always using other, stricter, condition before using these value. So it is safe to always carry them along.