Is there a file size limit for files attached to ipfs.infura.io?

The current limit is 100mb.

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When uploading a directory recursively with addFromFs, is the 100MB limit applied to each file, or to the whole request?

The limit is 100MB per request. Most of the API wrappers (including the one you are using) will do a single request when uploading a directory, effectively limiting the maximum size of a uploaded directory to 100MB.

We may have a smarter limiting in the future but it’s currently not so simple because IPFS doesn’t respect the multipat/form-data specification (see https://github.com/ipfs/ipfs/issues/395).