A Marin Superior Court judge on Tuesday finalized a ruling that pauses the lawsuit filed by Drakes Bay Oyster Company against the California Coastal Commission pending the resolution of the oyster farm’s federal litigation. Judge Lynn Duryee’s ruling protects Kevin Lunny’s operation from fines levied by the commission during that time, but does require him to comply with one section of a cease and desist order issued earlier this year, as well as a 2007 consent decree. Section 5 of the cease and desist order included production limits on oysters and clams, harbor seal protections, debris management requirements, requirements to remove an invasive tunicate known as didemnum from equipment and shellfish, a prohibition of non-sterile Manila clam seed and the removal of those clams from the estero. Mr. Lunny said lawyers were still working out exactly what the ruling means for the farm, but said that removal of the didemnum was “a biological and financial impossibility.” As for the clams, he said the order contradicts the 2007 decree, which allows Manila clam production. “If the court forces us to remove the Manila clams, we’ll do it. We’ll comply with the law. That’s what we do,” he said, adding that he thinks throwing away those clams would be wrong. The ruling is in response to two nearly identical lawsuits, one filed by biologist and Alliance for Sustainable Agriculture board member Phyllis Faber, the other by Drakes Bay Oyster Company, which were subsequently combined. The suit alleges that the California Coastal Commission violated the law when it issued the cease and desist and restoration orders earlier this year because the orders should have been subject to an environmental impact review as required by the California Environmental Quality Act.