Make the options for debug file and output file consistent with rest of CCTools.
Fix AllPairs tests to use the new option for output file.
Added -O as equivalent to --output-file
Update man page
Merge branch 'dpandiar-allpairsfix'

Fix confusion on what the -o option does. #352

Also updates tests to work with the new options.

Fixes #338.
Fix uninitialized variable errors reported by Valgrind.
Cleanup sand/test/TR_filter_verification.sh.

o Corrects whitespace.
o Uses more correct code (e.g. "$@").
o Fixes an error caused by sand/test/TR_filter_verification.sh changing directory.