Function resolve_edges 

pub fn resolve_edges(
    extracted: &mut ExtractedMemory,
    existing_node_ids: &HashSet<String>,
)

Populate graph_edges on an ExtractedMemory by checking which file graph nodes already exist in the database. This creates edges between files that were previously Read and are now being Edited or Written, capturing the common explore-then-modify workflow.

existing_node_ids should be the set of graph-node IDs already persisted (e.g. from storage.all_graph_nodes()).