How is it built? For example, if I built the same Linux kernel, it includes a counter that increments each assembly. GCC has options for using profiler information to control code generation if the profiling information changes, just like code.
What did you analyze? Generated assembly, objdump object files or executable? How did you compare the different versions? Are you sure you were looking for executable code, not compiler / assembler / linker timestamps?
Has anything changed in the environment? New libraries (and header / declaration / macro definition files!)? New compiler, linker? New kernel (yes, some header files are taken from the kernel source code and come with it)?
( , , , , IP-, )?
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