Why is the AVR GCC compiler using a full `CALL` even though I have set the `-mshort-calls` flag?
This option was removed in gcc 4.8 but not all the documentation was updated. Atmel Studio also still uses the obsolete flag. 

The new option is called -mrelax on the compiler command line or --relax on the linker command line...

https://gcc.gnu.org/onlinedocs/gcc-4.9.2/gcc/AVR-Options.html

After adding that flag, the above code compiled to...

...
3584:   00 d0           rcall   .+0         ; 0x3586 
3586:   f8 94           cli
...


If you are using Atmel Studio, the new flag is misleadingly called "Relax Branches" and is located here...



In my case, enabling relative jumps and calls resulted in significant flash savings. If you are here because you also need to save flash space and/or cycles, I'd also recommend looking into enabling Link Time Optimization which also offers great savings at no cost.