A workspace will contain a directory named compressed and a directory named uncompressed. You should only modify files in the uncompressed directory. GNTool is responsible for managing the compressed directory, workspace.bin file, and the optional codes.json file. Refreshing the workspace will detect any changes you've made to files in the uncompressed directory. Changes are detected by calculating the CRC32 hash of each file and comparing it against the last known CRC32 hash.