refactor (v2): better arch

Co-authored-by: Copilot <copilot@github.com>

crates/adapters/sqlite/migrations/20251226000000_create_note_links.sql

@@ -0,0 +1,12 @@
+CREATE TABLE IF NOT EXISTS note_links (
+    source_note_id TEXT NOT NULL,
+    target_note_id TEXT NOT NULL,
+    score REAL NOT NULL,
+    created_at DATETIME NOT NULL,
+    PRIMARY KEY (source_note_id, target_note_id),
+    FOREIGN KEY (source_note_id) REFERENCES notes(id) ON DELETE CASCADE,
+    FOREIGN KEY (target_note_id) REFERENCES notes(id) ON DELETE CASCADE
+);
+
+CREATE INDEX idx_note_links_source ON note_links(source_note_id);
+CREATE INDEX idx_note_links_target ON note_links(target_note_id);