There is no way to control the fact that the parser will generate a call to an atexit-related destructor registration routine for each global object with a destructor. However, you could minimize the added code by adding to your project a replacement function that does nothing. Are you using COFF ABI or EABI? If COFF ABI, the function is named _add_dtor; if EABI, the function is named __cxa_atexit. Note: this method is untested and unsupported.
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