Alignment Result: removes underlying intermediate results
BWA AR: check that intermediate results are removed
BWA AR: add user to intermedaite result right after creating
BWA AR: move intermediate params outside of each pass
BWA AR: update messages
BWA AR: use intermediate class directly instead of command class
BWA IAR: rm redundant command
AR: rm dumper statement
AR: store iar id to test removal
Alignment Result: add class for aligners having intermediate results