Don Porges fixed c99 issues.

configure.in

src/helper/command.c

src/helper/log.c

src/helper/replacements.c

src/helper/replacements.h

src/helper/time_support.c

src/helper/time_support.h

src/jtag/amt_jtagaccel.c

src/jtag/bitbang.c

src/jtag/bitq.c

src/jtag/ft2232.c

src/jtag/gw16012.c

src/jtag/jtag.c

src/jtag/presto.c