This commit addresses issues identified by LGTM for the various
independent (and mostly-independent) files in the Tools subdirectory.
The vast majority of the issues are trivial, and are things like unused
imports or catching BaseException. There was one true bug identified, a
global variable being changed in a function where it was not marked
global, but it only affected output quantity (the variable is named
"VERBOSE"). A couple of other issues identified variables that appear to
represent no-longer-existing options in the code. The options were left,
but a deprecation printout replaces the variable in the event the option
is provided.
