The Thonaris shipyards are a manufacturing and refueling shipyard facility in the Thonaris System, used by Omnius during the time of the Synchronized Worlds. Abandoned after the Butlerian Jihad, the facility remained idle until agents of Consolidated Transport discovered them, supposedly by accident.
Mentats Draigo Roget and Gilbertus Albertus had both surmised the existence of an the inactive manufacturing and refueling shipyard facility after studying shipping records from the days of the Synchronized Worlds. (Gilbertus later mentioned this to the Erasmus gelsphere, who confirmed that the Thonaris System did in fact host a large-scale operation.)
Acting on Draigo's mentat projection, Josef Venport acted on the information and sent an armed fleet of VenPort space craft to take control of the facility. There was rumor that Celestial Transport had already discovered the facility and had begun to utilize it to expand its space fleet. Upon arrival, Venport discovered that CT was using the facility, and its owner, Arjen Gates, was overseeing the operations. Venport quickly attacked and subdued the CT presence, with the added bonus of capturing (and subsequently killing) Arjen Gates, furthering the consolidation of space commerce for VenHold.
Using the knowledge of the existence of the shipyards as a bargaining chip to protect the Mentat school from Manford Torondo, Gilbertus shared his "projection" of the existence of the former machine facility to Manfred, who seized upon the opportunity to destroy the remnant of the Synchronized Worlds. Manfred led a Butlerian fleet of Jihad-era warships donated by Emperor Julius Corrino to destroy every trace of the facility. Upon arrival, they were surprised to discover that Venport had taken control, and was utililizing the facility to full capacity.