*Section 2*

I suggest that most of Section 2 might be placed in an appendix. The details of hash trees will not be of interest to most readers, and having a lot of text in this document devoted to those details may distract many readers. The details are critical to ensure interoperability and security, but a high level description of Merkle hash trees, audit paths, consistency proofs, etc. would suffice to explain to most readers how CT works. Moving details to a normative appendix would make the document easier to read.

Section 2.1.4 says that a log operator MUST use one of two specified signature algorithms with SHA-256. This implies that all clients MUST support both algorithms. I think it's important to justify this requirement, i.e., why are all clients forced to support both algorithms, while log operators get to choose which one they want to implement? Also, in many (thought not all) recent security area protocol designs, we have been separating the algorithm specs from the rest of the design, to accommodate algorithm agility. This document (or a companion) needs to address algorithm agility, irrespective of whether the algorithms are included here or elsewhere. I recall that the algorithm agility topic was raised but deferred in discussions on the list; I think it needs to be addressed, either here or in a companion document that is accepted by the WG as an essential element of the CT architecture. Also, there should be a discussion of how key rollover for logs is managed, once the topic of how to acquire log public keys is resolved.

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