migrate more files to use index-based node access

- learn.rs, daemon.rs, graph.rs, digest.rs, prompts.rs
- Convert store.nodes.get() → store.get_node()
- Convert store.nodes.contains_key() → store.contains_key()
- Convert store.nodes.values/iter() → all_keys + get_node

Co-Authored-By: Proof of Concept <poc@bcachefs.org>

src/subconscious/learn.rs

@@ -334,7 +334,9 @@ where
         for (i, node) in context.conversation().iter().enumerate() {
             if let Some(key) = memory_key(node) {
                 if !seen.insert(key.to_owned()) { continue; }
-                let last_scored = store.nodes.get(key)
+                let last_scored = store.get_node(key)
+                    .ok()
+                    .flatten()
                     .map(|n| n.last_scored)
                     .unwrap_or(0);
                 if now - last_scored >= max_age_secs {