incoming_paths SupplementalArena may not have an entry for every node
handle when the stitcher queries a node that was never the end_node of
any loaded path. Use .get() so out-of-range handles return Degree::Zero
instead of panicking with an index-out-of-bounds error.

… before stitching

Pre-loads all file-node paths and root paths from SQLite into the
in-memory Database before the stitcher runs. This ensures
incoming_paths is fully populated so get_incoming_path_degree returns
correct values for all nodes, preventing incorrect cycle-detection
behavior when using per-reference stitching.