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Revision for warnings and code structure #1

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Revised the code for:

  • Warnings: several warnings were removed from the code
  • Organization: code was reorganized in a standard way in order to facilitate future maintenance.
  • Build system:
    • Makefile review for better code organization
    • Added extra search paths to help the compiler find header files. On custom systems the original makefile was not finding the proper headers.

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