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Fixes: #40590

This commit updates gen_app_partitions.py to include only files present
in the current build by extracting the information from the CMake
generated `compile_commands.json` file.

This ensures that object files in sub-projects, such as `empty_cpu0`,
will not be considered by the script.

Using the compile_commands.json instead of walking the whole build tree
for finding object files also improves performance:

Time of executing `gen_app_partitions.py` (Old):
__________________________
Executed in  480.06 millis
   usr time  425.83 millis
   sys time   49.55 millis

Time of executing `gen_app_partitions.py` (New):
________________________________________________________
Executed in   76.22 millis
   usr time   49.00 millis
   sys time   24.59 millis
Signed-off-by: Torsten Rasmussen <Torsten.Rasmussen@nordicsemi.no>