A folder of three hundred files holds three hundred things and no relations. Your vault holds the shape: what came from what, and what was compared with what.
The vault is a graph
Every document a node, every link a synapse
The connectome is the form in which your vault is stored, and you navigate it on screen. Every upload adds a node; every translation or revision adds a node and the link back to its original; every comparison ties its two sides. You build nothing.
Links are declared, never guessed
A synapse exists because an operation recorded it
No link comes from computed similarity. Each one is recorded by the operation that created it, with what was done and on which version (your documents), so every edge has a receipt underneath. The engine does measure similarity, and tells you two decks are nearly the same, but that is a signal you read, not a link it draws.
Two readers, one network
You on screen; the agent from within
You enter through one document and reach its translations, revisions and comparisons. The agent reads the same network: it enters through one document, follows the links, and reads one section at a time, instead of swallowing every file at once. That is why its answer can come with a source: each passage never lost its address.
The network knows what you uploaded, and nothing beyond it. Where coverage ends is in the boundary.