Started adding analysis scripts to autotools

    * Makefile.am: Added analysis makefile
    * Makefile.in: Regenerated
    * analysis/Makefile.am: Automatically create simulate.avr
    * analysis/Makefile.in: Generated
    * analysis/simulate.avr: Deleted
    * analysis/simulate.avr.in: Created. Main body of simulate script.
    * configure: Regenerated
    * configure.ac: Added analysis makefile