As filed by @TexKiller as cloudflare/doca#77
If the project_folder is specified outside of the current directory, such as with doca init -i ../schemas -o ../documentation, the json schemas paths are messed up, ending up like ../../../schemas/schema.json.
The path to the schemas should be either absolute or relative to the project_folder, and not relative to the working directory.
As filed by @TexKiller as cloudflare/doca#77