I have a project that uses an '.S' file for the assembler code portion, the code is quite complex and it is not practical to use asm(). I have to place this in the library folder for it to be assembled and linked into my sketch. The assembler file requires a common header/configuration file with the C portion of the project. I must keep this in the library folder as well, so it will be found when included by both files. This means the configuration can not be maintained in the Arduino IDE.
I believe it should be possible to allow .S files to be edited in the IDE and assembled/linked from the project folder. It would be able to see project specific header files. The header file could be maintained as usual simplifying the use of my project/library. I think this can be done easily, just handle the .S the same way it is handled when found in the library folder.