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/hippocampus/store/mod.rs

@@ -33,6 +33,7 @@ pub use ops::current_provenance;
 use crate::graph::{self, Graph};
 
 use anyhow::{bail, Result};
+use redb::Database;
 
 /// Strip .md suffix from a key, handling both bare keys and section keys.
 /// "identity.md" → "identity", "foo.md#section" → "foo#section", "identity" → "identity"
@@ -120,34 +121,44 @@ impl Store {
         Ok(neighbors)
     }
 
+    /// Get the database for transaction management.
+    pub fn db(&self) -> Result<&Database> {
+        self.db.as_ref().ok_or_else(|| anyhow::anyhow!("store not loaded"))
+    }
+
     /// Remove a node from the index (used after appending a tombstone).
-    pub fn remove_from_index(&self, key: &str, uuid: &[u8; 16]) -> Result<()> {
-        if let Some(db) = self.db.as_ref() {
-            index::remove_node(db, key, uuid)?;
-        }
+    /// For batched operations, use index::remove_node with a WriteTransaction directly.
+    pub fn remove_from_index(&self, key: &str) -> Result<()> {
+        let db = self.db()?;
+        let txn = db.begin_write()?;
+        index::remove_node(&txn, key)?;
+        txn.commit()?;
         Ok(())
     }
 
     /// Get all edges for a node by UUID. Returns (other_uuid, strength, rel_type, is_outgoing).
     pub fn edges_for_uuid(&self, uuid: &[u8; 16]) -> Result<Vec<([u8; 16], f32, u8, bool)>> {
-        let db = self.db.as_ref()
-            .ok_or_else(|| anyhow::anyhow!("store not loaded"))?;
+        let db = self.db()?;
         index::edges_for_node(db, uuid)
     }
 
-    /// Add a relation to the index.
+    /// Add a relation to the index (opens its own transaction).
+    /// For batched operations, use index::index_relation with a WriteTransaction directly.
     pub fn index_relation(&self, source: &[u8; 16], target: &[u8; 16], strength: f32, rel_type: u8) -> Result<()> {
-        if let Some(db) = self.db.as_ref() {
-            index::index_relation(db, source, target, strength, rel_type)?;
-        }
+        let db = self.db()?;
+        let txn = db.begin_write()?;
+        index::index_relation(&txn, source, target, strength, rel_type)?;
+        txn.commit()?;
         Ok(())
     }
 
-    /// Remove a relation from the index.
+    /// Remove a relation from the index (opens its own transaction).
+    /// For batched operations, use index::remove_relation with a WriteTransaction directly.
     pub fn remove_relation_from_index(&self, source: &[u8; 16], target: &[u8; 16], strength: f32, rel_type: u8) -> Result<()> {
-        if let Some(db) = self.db.as_ref() {
-            index::remove_relation(db, source, target, strength, rel_type)?;
-        }
+        let db = self.db()?;
+        let txn = db.begin_write()?;
+        index::remove_relation(&txn, source, target, strength, rel_type)?;
+        txn.commit()?;
         Ok(())
     }