Leonard Clawson had several 19th c. patents for chimneys that mostly related to safety improvements. The Comstock House contract specs twice require "Clawson patent[s]" be used, and it's even fully written out on the blueprints. While Jones often specifies products that are trademarked or patented, this is the only time where "patent" is routinely used as part of the name.
On page 5, Jones specifies "Clawson patent arch bars" be used on the two fireplaces. Clawson's arch bar (1893 patent 502901) was a slightly curved metal bar that kept the fireplace shell snugly attached to the flue. Any gap between the two parts could lead to a house fire if sparks reached the plaster/lathe inner wall surrounding the chimney.
The specification, "Clawson patent 6 [inch] T.C. flues, with Galv. I. jackets where shown" is confusing because several things are being described in builder's shorthand. Jones was directing that both chimneys be constructed using one of Clawson's flue designs (presumably the 1890 patent 435557 for a flue with interlocking sections of terracotta pipe). The reception hall fireplace uses the main chimney, which was also shared with the kitchen stove. The galvanized iron stovepipe, connecting the kitchen with this chimney, can be seen by peeking through the unfinished kitchen spice cabinet. Note that Clawson's mailing label is still attached.
Clawson continued inventing well into the 20th century, bless 'im. He was awarded a 1901 patent (679666) for a chimney smoke condenser to reduce air pollution, and shared a 1921 patent (1370880) for a "deafening attachment for automobiles." Offices for L.E. Clawson & Co., Patent Chimneys and Sewer Pipe were at 1340 Market Street, San Francisco.