The C18 compiler will place all compiled object files in the project directory regardless of whether the source files are located there or in a subdirectory.
This makes building a project with subdirectories fail since the linker is unable to find the object files where it expects them to be (in the same subdirectory as the source file).
I could not find any way to add the necessary option, since the name of the object file is not exported as a variable. The attached patch fixes this and adds the option as default to the C18 toolchain.
Add %OBJECT to available command line macros
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I just committed your patch to the development sources.
Thanks and sorry for the long response time...
Nicolas