Merge pull request #50 from tgrrtt/develop

Implemented match and alternate removal
(fix) starts idNum at 0 on each new tree
(cleanup) cleaned modify-tree factory, railroad directive, and main controller
Merge pull request #51 from darkstar21/develop

Cleaned up modify tree factory, railroad directive, and main controller
Updated 'Alternate' removal

Can handle cases where parent is not an alternate.