All objects live in:

Selected (actual references)

Comps (actual references)

Clipboard (actual references)


Vertices keep arrays of components they're attached to - but this need not be stored.
Components keep track of what vertices they are attached to - this does need to be stored.
Components keep track of what high-level component they are part of.
High level parts have temporary (must be populated, but not saved) structures of what parts are part of them.