5.5 Cooking Doesn't Detect Content

My project’s Content folder contains directories leading to a single skeletal mesh, physics asset, and skeleton. These are the only assets in the entire project. When I cook content for windows, the end result is the exact same set of files I get when I cook a completely blank project: Four .json files and four .ushaderbytecode files. I want my mesh to be output as a .uasset and .uexp. Why might the cooker not be able to read my content folder? Thanks!