store: read nodes via index instead of HashMap

- Add get_node() and contains_key() methods that read via redb index
- Migrate all store/ reads to use index lookup
- Remove HashMap cache updates from mutations (write-through to capnp+index only)
- Remove replay_nodes() - load no longer builds HashMap
- Update db_is_healthy to validate by spot-checking offsets
- Fix set_weight bug: now persists weight changes to capnp

Store.nodes HashMap still exists for code outside store/ module,
but store/ itself no longer uses it.

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

src/hippocampus/store/capnp.rs

@@ -206,39 +206,79 @@ impl Relation {
     }
 }
 
+// ---------------------------------------------------------------------------
+// Direct node access
+// ---------------------------------------------------------------------------
+
+/// Read a single node at the given offset in the capnp log.
+/// The offset must point to a valid message containing the node.
+pub fn read_node_at_offset(offset: u64) -> Result<Node> {
+    let path = nodes_path();
+    let mut file = fs::File::open(&path)
+        .with_context(|| format!("open {}", path.display()))?;
+
+    use std::io::{Seek, SeekFrom};
+    file.seek(SeekFrom::Start(offset))?;
+
+    let mut reader = BufReader::new(file);
+    let msg = serialize::read_message(&mut reader, message::ReaderOptions::new())
+        .with_context(|| format!("read message at offset {}", offset))?;
+
+    let log = msg.get_root::<memory_capnp::node_log::Reader>()
+        .with_context(|| "read node log")?;
+    let nodes = log.get_nodes()
+        .with_context(|| "get nodes")?;
+
+    // A message at this offset should have exactly one node (from upsert),
+    // or we take the last one if there are multiple (from batch operations like rename)
+    if nodes.is_empty() {
+        anyhow::bail!("no nodes in message at offset {}", offset);
+    }
+
+    // Return the first non-deleted node, or the first one if all are deleted
+    for node_reader in nodes.iter() {
+        let node = Node::from_capnp_migrate(node_reader)?;
+        if !node.deleted {
+            return Ok(node);
+        }
+    }
+
+    // All nodes in this message are deleted - shouldn't happen if index is correct
+    Node::from_capnp_migrate(nodes.get(0))
+}
+
 // ---------------------------------------------------------------------------
 // Store persistence methods
 // ---------------------------------------------------------------------------
 
 impl Store {
-    /// Load store by replaying capnp logs, then open/verify redb indices.
+    /// Load store by opening redb index and replaying relations.
     pub fn load() -> Result<Store> {
         let nodes_p = nodes_path();
         let rels_p = relations_path();
 
         let mut store = Store::default();
 
-        if nodes_p.exists() {
-            store.replay_nodes(&nodes_p)?;
-        }
+        // Open redb index first (rebuilds from capnp if needed)
+        let db_p = db_path();
+        store.db = Some(store.open_or_rebuild_db(&db_p)?);
+
+        // Replay relations
         if rels_p.exists() {
             store.replay_relations(&rels_p)?;
         }
 
-        // Record log sizes after replay
+        // Record log sizes
         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|
-            store.nodes.contains_key(&r.source_key) &&
-            store.nodes.contains_key(&r.target_key)
+            index::contains_key(db, &r.source_key).unwrap_or(false) &&
+            index::contains_key(db, &r.target_key).unwrap_or(false)
         );
 
-        // Open redb and verify/rebuild indices
-        let db_p = db_path();
-        store.db = Some(store.open_or_rebuild_db(&db_p)?);
-
         Ok(store)
     }
 
@@ -263,80 +303,38 @@ impl Store {
         rebuild_index(path, &nodes_path())
     }
 
-    /// Check if redb indices match in-memory state.
+    /// Check if redb index is healthy by verifying some offsets are valid.
     fn db_is_healthy(&self, database: &redb::Database) -> Result<bool> {
-        use redb::ReadableDatabase;
+        use redb::{ReadableDatabase, ReadableTable};
 
         let txn = database.begin_read()?;
-
-        // Quick check: node count should match
         let nodes_table = txn.open_table(index::NODES)?;
-        let db_count = nodes_table.len()?;
 
-        if db_count != self.nodes.len() as u64 {
-            return Ok(false);
+        // Check that we can read the table and it has entries
+        if nodes_table.len()? == 0 {
+            // Empty database - might be stale or new
+            let capnp_size = fs::metadata(nodes_path()).map(|m| m.len()).unwrap_or(0);
+            return Ok(capnp_size == 0); // healthy only if capnp is also empty
         }
 
-        // Spot check: verify a few random nodes exist with matching keys
-        // (full verification would be too slow)
-        for (i, key) in self.nodes.keys().enumerate() {
-            if i >= 10 { break; } // check first 10
-            if nodes_table.get(key.as_str())?.is_none() {
+        // Spot check: verify a few offsets point to valid messages
+        let mut checked = 0;
+        for entry in nodes_table.iter()? {
+            if checked >= 5 { break; }
+            let (key, offset) = entry?;
+            let offset = offset.value();
+
+            // Try to read the node at this offset
+            if read_node_at_offset(offset).is_err() {
                 return Ok(false);
             }
+            checked += 1;
+            let _ = key; // silence unused warning
         }
 
         Ok(true)
     }
 
-    /// Replay node log, keeping latest version per UUID.
-    /// Tracks all UUIDs seen per key to detect duplicates.
-    fn replay_nodes(&mut self, path: &Path) -> Result<()> {
-        let file = fs::File::open(path)
-            .with_context(|| format!("open {}", path.display()))?;
-        let mut reader = BufReader::new(file);
-
-        // Track all non-deleted UUIDs per key to detect duplicates
-        let mut key_uuids: HashMap<String, Vec<[u8; 16]>> = HashMap::new();
-
-        while let Ok(msg) = serialize::read_message(&mut reader, message::ReaderOptions::new()) {
-            let log = msg.get_root::<memory_capnp::node_log::Reader>()
-                .with_context(|| format!("read node log"))?;
-            for node_reader in log.get_nodes()
-                .with_context(|| format!("get nodes"))? {
-                let node = Node::from_capnp_migrate(node_reader)?;
-                let existing_version = self.nodes.get(&node.key)
-                    .map(|n| n.version)
-                    .unwrap_or(0);
-                if node.version >= existing_version {
-                    if node.deleted {
-                        self.nodes.remove(&node.key);
-                        self.uuid_to_key.remove(&node.uuid);
-                        if let Some(uuids) = key_uuids.get_mut(&node.key) {
-                            uuids.retain(|u| *u != node.uuid);
-                        }
-                    } else {
-                        self.uuid_to_key.insert(node.uuid, node.key.clone());
-                        self.nodes.insert(node.key.clone(), node.clone());
-                        let uuids = key_uuids.entry(node.key).or_default();
-                        if !uuids.contains(&node.uuid) {
-                            uuids.push(node.uuid);
-                        }
-                    }
-                }
-            }
-        }
-
-        // Report duplicate keys
-        for (key, uuids) in &key_uuids {
-            if uuids.len() > 1 {
-                dbglog!("WARNING: key '{}' has {} UUIDs (duplicate nodes)", key, uuids.len());
-            }
-        }
-
-        Ok(())
-    }
-
     /// Replay relation log, keeping latest version per UUID
     fn replay_relations(&mut self, path: &Path) -> Result<()> {
         let file = fs::File::open(path)

src/hippocampus/store/mod.rs

@@ -76,15 +76,37 @@ impl Store {
         graph::build_graph(self)
     }
 
+    /// Get a node by key, reading from capnp via the index.
+    pub fn get_node(&self, key: &str) -> Result<Option<Node>> {
+        let db = self.db.as_ref()
+            .ok_or_else(|| anyhow::anyhow!("store not loaded"))?;
+
+        match index::get_offset(db, key)? {
+            Some(offset) => Ok(Some(capnp::read_node_at_offset(offset)?)),
+            None => Ok(None),
+        }
+    }
+
+    /// Check if a node exists by key.
+    pub fn contains_key(&self, key: &str) -> Result<bool> {
+        let db = self.db.as_ref()
+            .ok_or_else(|| anyhow::anyhow!("store not loaded"))?;
+        index::contains_key(db, key)
+    }
+
     pub fn resolve_key(&self, target: &str) -> Result<String> {
         // Strip .md suffix if present — keys no longer use it
         let bare = strip_md_suffix(target);
 
-        if self.nodes.contains_key(&bare) {
+        if self.contains_key(&bare)? {
             return Ok(bare);
         }
 
-        let matches: Vec<_> = self.nodes.keys()
+        let db = self.db.as_ref()
+            .ok_or_else(|| anyhow::anyhow!("store not loaded"))?;
+        let all_keys = index::all_keys(db)?;
+
+        let matches: Vec<_> = all_keys.iter()
             .filter(|k| k.to_lowercase().contains(&target.to_lowercase()))
             .cloned().collect();
 

src/hippocampus/store/ops.rs

@@ -2,7 +2,7 @@
 //
 // CRUD (upsert, delete), maintenance (decay, cap_degree), and graph metrics.
 
-use super::{index, types::*, Store};
+use super::{capnp, index, types::*, Store};
 
 use anyhow::{anyhow, bail, Result};
 use std::collections::{HashMap, HashSet};
@@ -17,7 +17,7 @@ pub fn current_provenance() -> String {
 impl Store {
     /// Add or update a node (appends to log + updates index).
     pub fn upsert_node(&mut self, mut node: Node) -> Result<()> {
-        if let Some(existing) = self.nodes.get(&node.key) {
+        if let Some(existing) = self.get_node(&node.key)? {
             node.uuid = existing.uuid;
             node.version = existing.version + 1;
         }
@@ -25,8 +25,6 @@ impl Store {
         if let Some(ref database) = self.db {
             index::index_node(database, &node.key, offset, &node.uuid)?;
         }
-        self.uuid_to_key.insert(node.uuid, node.key.clone());
-        self.nodes.insert(node.key.clone(), node);
         Ok(())
     }
 
@@ -39,9 +37,24 @@ impl Store {
 
     /// Recent nodes by provenance, sorted newest-first. Returns (key, timestamp).
     pub fn recent_by_provenance(&self, provenance: &str, limit: usize) -> Vec<(String, i64)> {
-        let mut nodes: Vec<_> = self.nodes.values()
-            .filter(|n| !n.deleted && n.provenance == provenance)
-            .map(|n| (n.key.clone(), n.timestamp))
+        let db = match self.db.as_ref() {
+            Some(db) => db,
+            None => return Vec::new(),
+        };
+        let keys = match index::all_keys(db) {
+            Ok(keys) => keys,
+            Err(_) => return Vec::new(),
+        };
+        let mut nodes: Vec<_> = keys.iter()
+            .filter_map(|key| {
+                let offset = index::get_offset(db, key).ok()??;
+                let node = capnp::read_node_at_offset(offset).ok()?;
+                if !node.deleted && node.provenance == provenance {
+                    Some((key.clone(), node.timestamp))
+                } else {
+                    None
+                }
+            })
             .collect();
         nodes.sort_by(|a, b| b.1.cmp(&a.1));
         nodes.truncate(limit);
@@ -60,11 +73,11 @@ impl Store {
 
     /// Upsert with explicit provenance (for agent-created nodes).
     pub fn upsert_provenance(&mut self, key: &str, content: &str, provenance: &str) -> Result<&'static str> {
-        if let Some(existing) = self.nodes.get(key) {
+        if let Some(existing) = self.get_node(key)? {
             if existing.content == content {
                 return Ok("unchanged");
             }
-            let mut node = existing.clone();
+            let mut node = existing;
             node.content = content.to_string();
             node.provenance = provenance.to_string();
             node.timestamp = now_epoch();
@@ -73,7 +86,6 @@ impl Store {
             if let Some(ref database) = self.db {
                 index::index_node(database, &node.key, offset, &node.uuid)?;
             }
-            self.nodes.insert(key.to_string(), node);
             Ok("updated")
         } else {
             let mut node = new_node(key, content);
@@ -82,8 +94,6 @@ impl Store {
             if let Some(ref database) = self.db {
                 index::index_node(database, &node.key, offset, &node.uuid)?;
             }
-            self.uuid_to_key.insert(node.uuid, node.key.clone());
-            self.nodes.insert(key.to_string(), node);
             Ok("created")
         }
     }
@@ -92,10 +102,10 @@ impl Store {
     pub fn delete_node(&mut self, key: &str) -> Result<()> {
         let prov = current_provenance();
 
-        let node = self.nodes.get(key)
+        let node = self.get_node(key)?
             .ok_or_else(|| anyhow!("No node '{}'", key))?;
         let uuid = node.uuid;
-        let mut deleted = node.clone();
+        let mut deleted = node;
         deleted.deleted = true;
         deleted.version += 1;
         deleted.provenance = prov;
@@ -104,7 +114,6 @@ impl Store {
         if let Some(ref database) = self.db {
             index::remove_node(database, key, &uuid)?;
         }
-        self.nodes.remove(key);
         Ok(())
     }
 
@@ -117,12 +126,11 @@ impl Store {
         if old_key == new_key {
             return Ok(());
         }
-        if self.nodes.contains_key(new_key) {
+        if self.contains_key(new_key)? {
             bail!("Key '{}' already exists", new_key);
         }
-        let node = self.nodes.get(old_key)
-            .ok_or_else(|| anyhow!("No node '{}'", old_key))?
-            .clone();
+        let node = self.get_node(old_key)?
+            .ok_or_else(|| anyhow!("No node '{}'", old_key))?;
 
         let prov = current_provenance();
 
@@ -164,10 +172,7 @@ impl Store {
             index::index_node(database, new_key, offset, &renamed.uuid)?;
         }
 
-        // Update in-memory cache
-        self.nodes.remove(old_key);
-        self.uuid_to_key.insert(renamed.uuid, new_key.to_string());
-        self.nodes.insert(new_key.to_string(), renamed);
+        // Update in-memory relations cache
         for updated in &updated_rels {
             if let Some(r) = self.relations.iter_mut().find(|r| r.uuid == updated.uuid) {
                 r.source_key = updated.source_key.clone();
@@ -261,10 +266,19 @@ impl Store {
     /// Set a node's weight directly. Returns (old, new).
     pub fn set_weight(&mut self, key: &str, weight: f32) -> Result<(f32, f32)> {
         let weight = weight.clamp(0.01, 1.0);
-        let node = self.nodes.get_mut(key)
+        let mut node = self.get_node(key)?
             .ok_or_else(|| anyhow!("node not found: {}", key))?;
         let old = node.weight;
+        if (old - weight).abs() < 0.001 {
+            return Ok((old, weight)); // unchanged
+        }
         node.weight = weight;
+        node.version += 1;
+        node.timestamp = now_epoch();
+        let offset = self.append_nodes(std::slice::from_ref(&node))?;
+        if let Some(ref database) = self.db {
+            index::index_node(database, key, offset, &node.uuid)?;
+        }
         Ok((old, weight))
     }
 
@@ -317,10 +331,10 @@ impl Store {
             bail!("link already exists: {} ↔ {}", source, target);
         }
 
-        let source_uuid = self.nodes.get(source)
+        let source_uuid = self.get_node(source)?
             .map(|n| n.uuid)
             .ok_or_else(|| anyhow!("source not found: {}", source))?;
-        let target_uuid = self.nodes.get(target)
+        let target_uuid = self.get_node(target)?
             .map(|n| n.uuid)
             .ok_or_else(|| anyhow!("target not found: {}", target))?;
 

src/hippocampus/store/view.rs

@@ -1,6 +1,6 @@
 // Read-only access abstraction for the memory store
 
-use super::types::*;
+use super::{capnp, index, types::*};
 use super::Store;
 
 // ---------------------------------------------------------------------------
@@ -19,21 +19,42 @@ pub trait StoreView {
 
     /// Node weight by key, or the default weight if missing.
     fn node_weight(&self, key: &str) -> f64;
-
-    /// Node content by key.
-    fn node_content(&self, key: &str) -> Option<&str>;
 }
 
 impl StoreView for Store {
     fn for_each_node<F: FnMut(&str, &str, f32)>(&self, mut f: F) {
-        for (key, node) in &self.nodes {
-            f(key, &node.content, node.weight);
+        let db = match self.db.as_ref() {
+            Some(db) => db,
+            None => return,
+        };
+        let keys = match index::all_keys(db) {
+            Ok(keys) => keys,
+            Err(_) => return,
+        };
+        for key in keys {
+            if let Ok(Some(offset)) = index::get_offset(db, &key) {
+                if let Ok(node) = capnp::read_node_at_offset(offset) {
+                    f(&key, &node.content, node.weight);
+                }
+            }
         }
     }
 
     fn for_each_node_meta<F: FnMut(&str, NodeType, i64)>(&self, mut f: F) {
-        for (key, node) in &self.nodes {
-            f(key, node.node_type, node.timestamp);
+        let db = match self.db.as_ref() {
+            Some(db) => db,
+            None => return,
+        };
+        let keys = match index::all_keys(db) {
+            Ok(keys) => keys,
+            Err(_) => return,
+        };
+        for key in keys {
+            if let Ok(Some(offset)) = index::get_offset(db, &key) {
+                if let Ok(node) = capnp::read_node_at_offset(offset) {
+                    f(&key, node.node_type, node.timestamp);
+                }
+            }
         }
     }
 
@@ -46,10 +67,10 @@ impl StoreView for Store {
 
     fn node_weight(&self, key: &str) -> f64 {
         let cfg = crate::config::get();
-        self.nodes.get(key).map(|n| n.weight as f64).unwrap_or(cfg.default_node_weight)
-    }
-
-    fn node_content(&self, key: &str) -> Option<&str> {
-        self.nodes.get(key).map(|n| n.content.as_str())
+        self.get_node(key)
+            .ok()
+            .flatten()
+            .map(|n| n.weight as f64)
+            .unwrap_or(cfg.default_node_weight)
     }
 }