store: index ops take WriteTransaction, mutations batch properly

Index functions now take &WriteTransaction instead of &Database,
allowing callers to batch multiple index operations in a single
transaction. Store mutations (upsert, delete, rename, etc.) now
begin_write/commit their own transactions, ensuring atomicity.

- replay_relations uses single txn for all relation indexing
- Store::db() exposes Database for callers needing txn control
- Convenience wrappers open their own txn for simple cases

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

src/cli/admin.rs

@@ -323,7 +323,7 @@ pub async fn cmd_dedup(apply: bool) -> Result<()> {
 
         // Remove doomed nodes from index
         for (doomed_node, _) in &copies[1..] {
-            store.remove_from_index(&doomed_node.key, &doomed_node.uuid)?;
+            store.remove_from_index(&doomed_node.key)?;
         }
 
         merged += doomed_uuids.len();