Fix layer grouping and nesting via document nodes

[Keavon]

Remove operations from tools and actions, like grouping/ungrouping and ordering shortcuts, layer visibility, layer deletion

All the ways a user can interact with the nested folder structures, for example CtrlG for grouping the selected layers, using the Select tool to Ctrl-click or double-click to dig down into the structure, etc. This issue involves porting all that behavior to the new nested folder structure in the node graph, which is the last step before deleting the old folder system to finally complete the migration to full nodes.