cmake build problem when building code for avr - cmake

Question

I am trying to build a sample project for avr atmega328p. And I am facing a strange issue. I have following directory structure.
inc/core/device_support.h
src/main.c
src/core/device_support.c
I have two project setups, one using make and another one using cmake. When I build using make everything works fine. but when I use cmake it doesn't compile ok. ( .text section is not same if I run avr-size -A myProject.elf and it doesn't run correctly on target mcu). But if I run the compile command manually in cmake project directory with build directory as working directory everything works fine.
I have narrowed down the problem to the fact that if we run compile command form core /home/user/avr/build/core it doesn't work, and If I run command while in /home/user/avr/build build directory It works fine. I have no clue to why this may be happening.
My question is why being on different directory messes up compilation and how can I fix it in cmake.
with make I have something like:
avr-gcc -DARDUINO=10808 -DF_CPU=160000000L -I/home/user/avr/inc/core -mmcu=atmega328p -ffunction-sections -fdata-sections -MMD -flto -std=gnu11 -fno-fat-lto-objects -Os -w -g -MD -MT /home/user/avr/src/core/device_support.c -o /home/user/avr/build/core/device_support.o
and with cmake auto generated script I have:
cd /home/user/avr/build/core && avr-gcc -DARDUINO=10808 -DF_CPU=160000000L -I/home/user/avr/inc/core -mmcu=atmega328p -ffunction-sections -fdata-sections -MMD -flto -std=gnu11 -fno-fat-lto-objects -Os -w -g -MD -MT -o src/CMakeFiles/core.dir/src/core/device_support.o /home/user/avr/src/core/device_support.c
UPDATE 01:
avr-size -A myProject.elf output (cmake):
section size addr
.data 0 8388864
.text 740 0
.bss 9 8388864
.comment 17 0
.note.gnu.avr.deviceinfo 64 0
.debug_aranges 120 0
.debug_info 3537 0
.debug_abbrev 1965 0
.debug_line 1044 0
.debug_frame 124 0
.debug_str 1175 0
.debug_loc 843 0
.debug_ranges 40 0
Total 9678
avr-size -A myProject.elf output (make):
section size addr
.data 0 8388864
.text 930 0
.bss 9 8388864
.comment 17 0
.note.gnu.avr.deviceinfo 64 0
.debug_aranges 104 0
.debug_info 3559 0
.debug_abbrev 2002 0
.debug_line 1134 0
.debug_frame 180 0
.debug_str 1139 0
.debug_loc 1154 0
.debug_ranges 24 0
Total 10316
You can see the difference in .text section. Its a simple led blink code When I run this on device in cmake case LED stays on at sometimes and completely off at others. And If I compile the same code manually by running the same commands from cmake's output, but with build directory as my working directory then LED blinks as expected.
There are no errors during build in either case. The only difference is being in build directory. If I build manually and my working directory is not build then It fails in this case as well. For some reason being in build directory during compilation is important and I have no clue why.
Update 02:
Example code has been upload to : https://github.com/systemangle/mcve_avr
Please see project readme.

Answer 1

For some reason being in build directory during compilation is important and I have no clue why
Then you probably already have the answer. The problem doesn't seem to be CMake related.
May be you can try an in-source build with cmake and see what happen.
Otherwise if you want to mimic the hand-written Makefile behaviour you can avoid using any add_subdirectory and only write a big fat CMakeLists.txt at the root of your project.
All that said, if compilation output vary depending on where you are when the compiler is invoked then I think you'd better off asking question to the people providing the cross-compiler about this weird behavior.
Did you try hand compilation a file while being in a different directory?
Does this change the outputed object file?