Removed commas from options output

The rest of the options don’t have commas.  Consistency is nice. :)
Align long-options in help for better readability
Grouped Output and Search options separately
Tweaked option groups
Cleanup unused variable.
Remove unnecessary assignment.
Use malloc wrapper.
Use correct integer type in format string.
Quote the $@ variable passed to ./configure

Allows build.sh to be invoked with complex arguments to be passed to
configure script e.g.
- ./build.sh CFLAGS='-O3 -fomit-frame-pointer -s' CC=clang
Merge pull request #286 from mcphail/build_sh_pass_vars

Quote the $@ variable passed to ./configure
Merge pull request #274 from rrebello/ag_fixes

Misc fixes
Merge pull request #258 from Zearin/3.grouped_options

Improved `--help` output
Kill trailing whitespace.