Hi Totem,
I have the same issue here, if you have a solution in the meantime let me know plz…
What I understand about it till now is that the files-api (MFS) can be used if you want to assemble (and in this process of assembly you can rename or remove or move your files etc.) a file-stucture. When you are done you can get the CIDhash with ipfs.files.stat. (you can get the hash so easily because the files-api (MFS) is connected to the (regular) files-api, so what is saved in MFS is also put on IPFS automatically).
If you want to change something later, this is not easy/possible. I would think you have to first fetch the files from IPFS to put them in MFS (I didn’t figure out how that is possible (I have tried .read .cat and .get and they all do not save the files in the MFS “sandbox”)
The object-api can be used to make a data-structure (dag IPLD). In the structure you can put nodes containing property values and/or links to another node. I understand there is a 4mb size limit to files you ad with a buffer (I got this answer from Volker last time). Maybe we can get around this by creating a separate file cid first, and then ad it to the data-structure. Never mind… with the object.patch.setData you can update your property values and get a the hash back without having to download the whole data-structure.
I hope this can help anyone 