My first thought is to think of this as a tree structure. Not that my first thoughts are always right ...

Suppose you have a hash of root tree nodes. The key to the root node hash is one of your matches. Each node is itself a hash, containing several things: The line number, a (possibly undefined) reference to the next node in the tree, and anything else you may need. As you parse each element (each line), you take each match of that element and look it up by starting at the top of the tree: You do a lookup in the root node hash. If you find a hit, you follow the next node references down to the end, and add a new node. If you don't find a hit, you add a new element to the root hash. I believe this could also be optmized by keeping a last node hash. To get your relationships, you traverse each root node down when you're done.

Update: Actually, I'm not sure this truly handles all the relationships that elegantly. At a minimum, each node would have to be an array of other (sub)nodes to get all the relationships. It seems like there should be a simpler way to do that.