First pass at a bonding plugin

Change-Id: I081f592f598b77794366493ba90f5dedc4fa4dbc
Port to Qt 5, add clear bond action

This now has a simple bond perception routine, GUI could be added
to configure parameters. All bonds can also be removed from the
molecule.

Change-Id: Ibddf3c1f7cca9dd5dc8ff4a074a4e82d3d429f2c
Merge branch 'bonding-extension'

Change-Id: Icbcfe11896dc3209f5f39fb8eba1ad7653209220