Rewrite Makefile to resolve dependency issues reported by Vemake #1539
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Hi, we found 16 missing dependencies in the Makefile.
The eeprom.o depends on eeprom.c but no other headers specified in the Makefile.
We have rewritten the Makefile to take the input from the .d files generated from Auto Dependency Generation.
Please have a look.
This PR also fix missing dependencies reported in #1537
Thanks