in cli the filenames controlled by user
fixed \s+ split Sequence strings - test pass
input output file args in main - fixed
more informative error msgs
Added issues/ test xml files based on live run

see test/data/issues/issues.txt
Merge remote-tracking branch 'origin/after_the_hack' into cleanup_validate_remove_extra

Conflicts:
	src/org/sbols/converter/SBOLConverter.java
added tests Features that are Already Subparts
PartsRegistryDnaComponent.addRegistry_type rename

no "s", single
PartsRegistryDnaComponent.addRegistry_type rename

no "s", single
debug and separate "already a subpart"

and
PartsRegistryDnaComponent.addRegistry_type rename
no "s", single
separating out endstart/ tests
Feature tests grouped into categories
Test for Feature AlreadyASubPart - expect merge into 1 SA-DC result
TitleBBa Already A SubPart Feature is now merged with the SubPart