store: remove Vec<Relation>, dedup uses index iteration

The relations Vec is gone from Store. dedup now iterates via
edges_for_uuid() instead of mutating in-memory Vec — removes/re-adds
edges through the index directly.

Removed load_relations_vec() and clear_relations() — no longer needed.
Added helper methods: edges_for_uuid, index_relation, remove_relation_from_index.

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

src/cli/admin.rs

@@ -113,7 +113,7 @@ pub async fn cmd_fsck() -> Result<()> {
 }
 
 pub async fn cmd_dedup(apply: bool) -> Result<()> {
-    use std::collections::{HashMap, HashSet};
+    use std::collections::HashMap;
 
     let arc = memory::access_local()?;
     let mut store = arc.lock().await;
@@ -210,6 +210,14 @@ pub async fn cmd_dedup(apply: bool) -> Result<()> {
         .chain(diverged_groups)
         .collect();
 
+    // Build uuid → key map for relation key strings
+    let mut uuid_to_key: HashMap<[u8; 16], String> = HashMap::new();
+    for key in store.all_keys()? {
+        if let Ok(Some(node)) = store.get_node(&key) {
+            uuid_to_key.insert(node.uuid, key);
+        }
+    }
+
     let mut merged = 0usize;
     let mut edges_redirected = 0usize;
     let mut edges_deduped = 0usize;
@@ -219,52 +227,89 @@ pub async fn cmd_dedup(apply: bool) -> Result<()> {
         copies.sort_by(|a, b| b.1.cmp(&a.1).then(b.0.version.cmp(&a.0.version)));
 
         let survivor_uuid = copies[0].0.uuid;
+        let survivor_key = uuid_to_key.get(&survivor_uuid).cloned().unwrap_or_default();
         let doomed_uuids: Vec<[u8; 16]> = copies[1..].iter().map(|c| c.0.uuid).collect();
 
-        // Redirect edges from doomed UUIDs to survivor
-        let mut updated_rels = Vec::new();
-        for rel in &mut store.relations {
-            if rel.deleted { continue; }
-            let mut changed = false;
-            if doomed_uuids.contains(&rel.source) {
-                rel.source = survivor_uuid;
-                changed = true;
-            }
-            if doomed_uuids.contains(&rel.target) {
-                rel.target = survivor_uuid;
-                changed = true;
-            }
-            if changed {
-                rel.version += 1;
-                updated_rels.push(rel.clone());
+        // Redirect edges from doomed UUIDs to survivor via index iteration
+        for doomed_uuid in &doomed_uuids {
+            let edges = store.edges_for_uuid(doomed_uuid)?;
+            for (other_uuid, strength, rel_type, is_outgoing) in edges {
+                let other_key = uuid_to_key.get(&other_uuid).cloned().unwrap_or_default();
+
+                // Remove old edge from index
+                let (old_src, old_tgt) = if is_outgoing {
+                    (*doomed_uuid, other_uuid)
+                } else {
+                    (other_uuid, *doomed_uuid)
+                };
+                store.remove_relation_from_index(&old_src, &old_tgt, strength, rel_type)?;
+
+                // Add redirected edge
+                let (new_src, new_tgt, src_key, tgt_key) = if is_outgoing {
+                    (survivor_uuid, other_uuid, survivor_key.clone(), other_key)
+                } else {
+                    (other_uuid, survivor_uuid, other_key, survivor_key.clone())
+                };
+                store.index_relation(&new_src, &new_tgt, strength, rel_type)?;
+
+                // Append tombstone for old + new relation to log
+                let mut tombstone = store::new_relation(
+                    old_src, old_tgt,
+                    store::RelationType::from_u8(rel_type), strength,
+                    &uuid_to_key.get(&old_src).cloned().unwrap_or_default(),
+                    &uuid_to_key.get(&old_tgt).cloned().unwrap_or_default(),
+                );
+                tombstone.deleted = true;
+                tombstone.version = 2;
+
+                let mut redirected = store::new_relation(
+                    new_src, new_tgt,
+                    store::RelationType::from_u8(rel_type), strength,
+                    &src_key, &tgt_key,
+                );
+                redirected.version = 2;
+
+                store.append_relations(&[tombstone, redirected])?;
                 edges_redirected += 1;
             }
         }
 
-        // Dedup edges: same (source, target, rel_type) → keep highest strength
-        let mut seen: HashSet<([u8; 16], [u8; 16], String)> = HashSet::new();
-        let mut to_tombstone_rels = Vec::new();
-        // Sort by strength descending so we keep the strongest
-        let mut rels_with_idx: Vec<(usize, &store::Relation)> = store.relations.iter()
-            .enumerate()
-            .filter(|(_, r)| !r.deleted && (r.source == survivor_uuid || r.target == survivor_uuid))
-            .collect();
-        rels_with_idx.sort_by(|a, b| b.1.strength.total_cmp(&a.1.strength));
+        // Dedup edges: same (other_uuid, rel_type) → keep highest strength
+        // Group edges by (other, type), sort each group by strength desc, tombstone extras
+        let edges = store.edges_for_uuid(&survivor_uuid)?;
+        let mut by_endpoint: HashMap<([u8; 16], u8), Vec<(f32, bool)>> = HashMap::new();
+        for (other_uuid, strength, rel_type, is_outgoing) in edges {
+            by_endpoint.entry((other_uuid, rel_type))
+                .or_default()
+                .push((strength, is_outgoing));
+        }
 
-        for (idx, rel) in &rels_with_idx {
-            let edge_key = (rel.source, rel.target, format!("{:?}", rel.rel_type));
-            if !seen.insert(edge_key) {
-                to_tombstone_rels.push(*idx);
+        for ((other_uuid, rel_type), mut variants) in by_endpoint {
+            if variants.len() <= 1 { continue; }
+            // Sort by strength descending, keep first
+            variants.sort_by(|a, b| b.0.total_cmp(&a.0));
+            let other_key = uuid_to_key.get(&other_uuid).cloned().unwrap_or_default();
+
+            for (strength, is_outgoing) in variants.into_iter().skip(1) {
+                let (src, tgt, src_key, tgt_key) = if is_outgoing {
+                    (survivor_uuid, other_uuid, survivor_key.clone(), other_key.clone())
+                } else {
+                    (other_uuid, survivor_uuid, other_key.clone(), survivor_key.clone())
+                };
+                store.remove_relation_from_index(&src, &tgt, strength, rel_type)?;
+
+                let mut tombstone = store::new_relation(
+                    src, tgt,
+                    store::RelationType::from_u8(rel_type), strength,
+                    &src_key, &tgt_key,
+                );
+                tombstone.deleted = true;
+                tombstone.version = 2;
+                store.append_relations(&[tombstone])?;
                 edges_deduped += 1;
             }
         }
 
-        for &idx in &to_tombstone_rels {
-            store.relations[idx].deleted = true;
-            store.relations[idx].version += 1;
-            updated_rels.push(store.relations[idx].clone());
-        }
-
         // Tombstone doomed nodes
         let mut tombstones = Vec::new();
         for (doomed_node, _) in &copies[1..] {
@@ -275,9 +320,6 @@ pub async fn cmd_dedup(apply: bool) -> Result<()> {
         }
 
         store.append_nodes(&tombstones)?;
-        if !updated_rels.is_empty() {
-            store.append_relations(&updated_rels)?;
-        }
 
         // Remove doomed nodes from index
         for (doomed_node, _) in &copies[1..] {
@@ -287,9 +329,6 @@ pub async fn cmd_dedup(apply: bool) -> Result<()> {
         merged += doomed_uuids.len();
     }
 
-    // Remove tombstoned relations from cache and rebuild index
-    store.relations.retain(|r| !r.deleted);
-    store.reindex_relations()?;
     store.save()?;
 
     println!("Merged {} duplicates, redirected {} edges, deduped {} duplicate edges",

src/hippocampus/store/capnp.rs

@@ -272,12 +272,7 @@ impl Store {
         store.loaded_nodes_size = fs::metadata(&nodes_p).map(|m| m.len()).unwrap_or(0);
         store.loaded_rels_size = fs::metadata(&rels_p).map(|m| m.len()).unwrap_or(0);
 
-        // Drop edges referencing deleted/missing nodes
-        let db = store.db.as_ref().unwrap();
-        store.relations.retain(|r|
-            index::contains_key(db, &r.source_key).unwrap_or(false) &&
-            index::contains_key(db, &r.target_key).unwrap_or(false)
-        );
+        // Orphan edges filtered naturally during for_each_relation (unresolvable UUIDs skipped)
 
         Ok(store)
     }
@@ -359,13 +354,10 @@ impl Store {
             }
         }
 
-        self.relations = by_uuid.into_values()
-            .filter(|r| !r.deleted)
-            .collect();
-
-        // Index relations in redb
+        // Index relations directly (no Vec intermediate)
         if let Some(db) = &self.db {
-            for rel in &self.relations {
+            for rel in by_uuid.into_values() {
+                if rel.deleted { continue; }
                 index::index_relation(db, &rel.source, &rel.target, rel.strength, rel.rel_type as u8)?;
             }
         }

src/hippocampus/store/index.rs

@@ -209,18 +209,6 @@ pub fn remove_relation(
     Ok(())
 }
 
-/// Clear all relations from the index.
-pub fn clear_relations(db: &Database) -> Result<()> {
-    let txn = db.begin_write()?;
-    {
-        // Drop and recreate the table
-        txn.delete_multimap_table(RELS)?;
-        let _ = txn.open_multimap_table(RELS)?;
-    }
-    txn.commit()?;
-    Ok(())
-}
-
 /// Get all edges for a node. Returns (other_uuid, strength, rel_type, is_outgoing).
 pub fn edges_for_node(db: &Database, node_uuid: &[u8; 16]) -> Result<Vec<([u8; 16], f32, u8, bool)>> {
     let txn = db.begin_read()?;

src/hippocampus/store/mod.rs

@@ -47,7 +47,6 @@ pub fn strip_md_suffix(key: &str) -> String {
 
 // The full in-memory store
 pub struct Store {
-    pub relations: Vec<Relation>,              // all active relations
     /// Log sizes at load time — used for staleness detection.
     pub(crate) loaded_nodes_size: u64,
     pub(crate) loaded_rels_size: u64,
@@ -58,7 +57,6 @@ pub struct Store {
 impl Default for Store {
     fn default() -> Self {
         Store {
-            relations: Vec::new(),
             loaded_nodes_size: 0,
             loaded_rels_size: 0,
             db: None,
@@ -130,14 +128,25 @@ impl Store {
         Ok(())
     }
 
-    /// Rebuild relation index from Vec. Call after mutations that modify relations.
-    pub fn reindex_relations(&self) -> Result<()> {
-        if let Some(db) = self.db.as_ref() {
-            index::clear_relations(db)?;
-            for rel in &self.relations {
-                if rel.deleted { continue; }
-                index::index_relation(db, &rel.source, &rel.target, rel.strength, rel.rel_type as u8)?;
+    /// 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"))?;
+        index::edges_for_node(db, uuid)
     }
+
+    /// Add a relation to the index.
+    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)?;
+        }
+        Ok(())
+    }
+
+    /// Remove a relation from the index.
+    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)?;
         }
         Ok(())
     }

src/hippocampus/store/ops.rs

@@ -28,13 +28,12 @@ impl Store {
         Ok(())
     }
 
-    /// Add a relation (appends to log + updates cache + indexes)
+    /// Add a relation (appends to log + indexes)
     pub fn add_relation(&mut self, rel: Relation) -> Result<()> {
         self.append_relations(std::slice::from_ref(&rel))?;
         if let Some(db) = &self.db {
             index::index_relation(db, &rel.source, &rel.target, rel.strength, rel.rel_type as u8)?;
         }
-        self.relations.push(rel);
         Ok(())
     }