Where do class files go in Sloeber Eclipse project?
With Sloeber Eclipse plugin the ino files go to root of the project and the cpp, c and h files can be in root or in subfolders. example:



Folders created by Sloeber: core subfolder is a virtual folder with links to Arduino core files and variant files of the selected board. libraries folder is a virtual folder with links to libraries selected for the project. Release folder contains the generated make file, the .o files and the resulting elf, hex, bin files. (And sloeber.ino.cpp is a file generated by Sloeber)

Project folders: data folder in example picture is a convention for a folder with esp8266 SPIFFS files. utility is a subfolder with additional source files of the project.