put check in runParallelShellCommands for empty list tho im not sure if this is the issue
fix bug in halAlignability and halPhyloPMain where more than the total length could be computed due to a bug in chopping into sequence coordinates
change recursive traversal in columnIterator and mappedSegment to not visit paralogy edges when parent genome is not within scope.  thus hopefully correcting a longstanding bug.
Merge remote-tracking branch 'refs/remotes/origin/development' into modificationTools
Add "merge" option to halAppendSubtree

Using the option will merge the appended node and the node which is
appended to.

This makes halAddToNode unnecessary (this is more general) so I
removed it.