Originally the French had decided that yachts arriving from the UK would have to check in at designated ports of entry.
However, following discussions with the authorities & the Cruising association, it has now been agreed that sailors can go straight to any French port.
I am not sure how the process will work exactly but will advise when I know.
In the meantime here is a confirmatory link from the Yachting monthly
Update
Whilst there was an agreement that yachts could enter a variety of ports, it was unclear how the customs system would work for getting passports stamped for entry & departure of the schengan zone. For instance:- if one entered via Boulogne one has to then go via train, bus, or taxi, to Calais to go through the customs procedures. This is clearly a lengthy time wasting effort & one might consider it easier to sail to Calais in the first instance. Similarly, Dieppe has no specific customs office set up for UK travellers. It is not clear whether the ferry customs post will process yachtsmen’s documents, when open for ferry arrivals.
It is , therefore, suggested that, inspite of the press release in the link above, mariners make enquiries, with the port they intend to visit, before travelling.