I've spent the best part of the day checking German, English and Russian publications and some things seem universally agreed on:
1. Pirelli sent out an Email to all teams in Apr. 2012 telling them that the rules allow 1.000km tire tests and if teams were interested they should contact Pirelli.
So far, so good. But that email, which is claimed to have been seen by autosport.com and Motorsport Total, does not mention the use of a current car. Checking against the regulations, every team lawyer worth his salary must come to the conclusion that these tests will have to be done with cars that are at least 2 seasons old. (2011 cars in 2013). So Pirelli satisfied the pre-requirement to offer the test to all teams, but didn't communicate their full intentions.
2. FOTA reacted to Pirelli email and advised teams that in-season tests are not permitted
Only days after the Pirelli EMail another one made the rounds. That one, again claimed to have been read by aforementioned publications, came from FOTA. They advised the teams that an in-season 1.000km test as offered by Pirelli would only be acceptable if the rules were amended after unanimous decision by all teams. Such decision was never taken, so the issue is pretty unambiguous - it's forbidden. full stop.
After Bahrain 2013 1.000 km tests were independently offered to Ferrari, Mercedes and Red Bull
This is where it gets messy. Pirelli obviously renewed the offer with tentative blessing from FIA, probably citing safety issues as the reason (delaminations). Whether this blessing was a gentlemen's agreement, exists in writing or is purely a product of Pirelli's imagination - your guess is as good as mine. Ferrari accepted the offer and, following the regulations, ran a test with a 2011 car and Pedro de la Rosa at the wheel in Bahrain. Red Bull declined the offer. Like Ferrari they assumed that a 2011 car had to be used and since the 2011 car relied heavily on the trick diffusor, any data gathered with it would have little relevance to their 2013 contender. This is my speculation as I severely doubt RB would have declined a 2013 test if it was legal.
Mercedes ran the test with their current cars driven by Nico Rosberg and Lewis Hamilton from Wed. 15th to Friday 17th of May. This should explain, why the other teams didn't notice anything. Merc packed up and sneaked back in two days later, when all others were gone. But even if they left their stuff unpacked. It's not any other teams job to keep tabs on when Merc leaves, where for and when.
The real stinker here is, that the same renewed offer was not made to the likes of Lotus, Sauber etc. Pirelli is clearly playing favourites and that alone is every reason to not renew their contract. F1 has enough problems as it is - adding a corrupt supplier to that list isn't really what it needs.
Mercedes claims they didn't gain any advantage over their competitors
Yeah, sure Ross and pigs fly. If Mercedes didn't expect to gain anything from the test, why didn't they use a test and development driver, like Ferrari. They used their current car driven by their current drivers, who covered three whole GP distances on an actual race track partially on the tires that will be introduced in Canada. If nothing else, just the track time for the drivers is worth a lot already.
As far as information are available, there were no FIA scrutineers present, who made sure that Mercedes ran the cars in exactly the same specification as in the Spanish GP, so the chance is they tested some upcoming upgrades. One Italian journo claims they tested a modified rear suspension, but nobody else picked up on that so far, so it is probably just wild speculation by a Ferrari worshiper.
My conclusion
Pirelli did it again. They massively effed up F1 and put the FIA into an impossible situation. They knowingly (and therefore deliberately) breached the rules and Mercedes went along with it. That might be acceptable business practice in some shadier neighbourhoods of Palermo, but not in a multi-million dollar business like F1.
What is FIA supposed to do? If they hand out harsh punishment, they'll alienate one of the two major works teams and one of the three big engine suppliers. If they let it go unpunished RB and Ferrari will go apeshyte. If they hand out a fine, Mateschitz will send a big wad of cash and RB goes in-season testing.
Pirelli's intentions are not that hard to read. They've complained very vocally lately about the lack of testing. When they didn't get what they wanted, they just took matters in their own hands. Well, newsflash Paul, if you want a new contract for 2014, blackmailing your negotiation partners ain't the way to get it. Quite frankly, after the ridiculous 2013 tyres and this latest episode, I've come to the conclusion that a renewal of Pirelli's contract would be catastrophic for F1.