A cost matrix is a way of representing the cost of each individual tile in a room for a pathfinding algorithm like A* or Dijkstra’s.
Internally, it’s simply a list of 2500 unsigned integers (one for each tile). The built-in Pathfinder uses a 8-bit integers (0-255).
Clockwork uses the LocalCostMatrix from screeps-game-api internally, but exposes a ClockworkCostMatrix class with get and set methods similar to PathFinder.CostMatrix. These have approximately the same cost as the PathFinder version, but you’ll need to make sure you clean up the ClockworkCostMatrix with .free() when you don’t need it any more - it won’t be garbage-collected automatically.