consciousness/poc-memory/src/store/persist.rs

// Persistence layer: load, save, replay, append, snapshot
//
// Three-tier loading strategy:
//   1. rkyv mmap snapshot (snapshot.rkyv) — ~4ms deserialize
//   2. bincode cache (state.bin) — ~10ms
//   3. capnp log replay — ~40ms
//
// Logs are append-only; cache staleness uses log file sizes, not mtimes.

use super::types::*;

use crate::memory_capnp;

use capnp::message;
use capnp::serialize;

use std::collections::HashMap;
use std::fs;
use std::io::{BufReader, BufWriter, Seek};
use std::path::Path;

impl Store {
    /// Load store from state.bin cache if fresh, otherwise rebuild from capnp logs.
    ///
    /// Staleness check uses log file sizes (not mtimes). Since logs are
    /// append-only, any write grows the file, invalidating the cache.
    /// This avoids the mtime race that caused data loss with concurrent
    /// writers (dream loop, link audit, journal enrichment).
    pub fn load() -> Result<Store, String> {
        // 1. Try rkyv mmap snapshot (~4ms with deserialize, <1ms zero-copy)
        match Self::load_snapshot_mmap() {
            Ok(Some(mut store)) => {
                // rkyv snapshot doesn't include visits — replay from log
                let visits_p = visits_path();
                if visits_p.exists() {
                    store.replay_visits(&visits_p).ok();
                }
                return Ok(store);
            },
            Ok(None) => {},
            Err(e) => eprintln!("rkyv snapshot: {}", e),
        }

        // 2. Try bincode state.bin cache (~10ms)
        let nodes_p = nodes_path();
        let rels_p = relations_path();
        let state_p = state_path();

        let nodes_size = fs::metadata(&nodes_p).map(|m| m.len()).unwrap_or(0);
        let rels_size = fs::metadata(&rels_p).map(|m| m.len()).unwrap_or(0);

        if let Ok(data) = fs::read(&state_p) {
            if data.len() >= CACHE_HEADER_LEN && data[..4] == CACHE_MAGIC {
                let cached_nodes = u64::from_le_bytes(data[4..12].try_into().unwrap());
                let cached_rels = u64::from_le_bytes(data[12..20].try_into().unwrap());

                if cached_nodes == nodes_size && cached_rels == rels_size {
                    if let Ok(mut store) = bincode::deserialize::<Store>(&data[CACHE_HEADER_LEN..]) {
                        // Rebuild uuid_to_key (skipped by serde)
                        for (key, node) in &store.nodes {
                            store.uuid_to_key.insert(node.uuid, key.clone());
                        }
                        store.loaded_nodes_size = nodes_size;
                        store.loaded_rels_size = rels_size;
                        // Bootstrap: write rkyv snapshot if missing
                        if !snapshot_path().exists() {
                            if let Err(e) = store.save_snapshot(cached_nodes, cached_rels) {
                                eprintln!("rkyv bootstrap: {}", e);
                            }
                        }
                        return Ok(store);
                    }
                }
            }
        }

        // Stale or no cache — rebuild from capnp logs
        let mut store = Store::default();

        if nodes_p.exists() {
            store.replay_nodes(&nodes_p)?;
        }
        if rels_p.exists() {
            store.replay_relations(&rels_p)?;
        }
        let visits_p = visits_path();
        if visits_p.exists() {
            store.replay_visits(&visits_p)?;
        }

        // Record log sizes after replay — this is the state we reflect
        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
        store.relations.retain(|r|
            store.nodes.contains_key(&r.source_key) &&
            store.nodes.contains_key(&r.target_key)
        );

        store.save()?;
        Ok(store)
    }

    /// 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<(), String> {
        let file = fs::File::open(path)
            .map_err(|e| format!("open {}: {}", path.display(), e))?;
        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>()
                .map_err(|e| format!("read node log: {}", e))?;
            for node_reader in log.get_nodes()
                .map_err(|e| format!("get nodes: {}", e))? {
                let node = Node::from_capnp(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 {
                eprintln!("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<(), String> {
        let file = fs::File::open(path)
            .map_err(|e| format!("open {}: {}", path.display(), e))?;
        let mut reader = BufReader::new(file);

        // Collect all, then deduplicate by UUID keeping latest version
        let mut by_uuid: HashMap<[u8; 16], Relation> = HashMap::new();

        while let Ok(msg) = serialize::read_message(&mut reader, message::ReaderOptions::new()) {
            let log = msg.get_root::<memory_capnp::relation_log::Reader>()
                .map_err(|e| format!("read relation log: {}", e))?;
            for rel_reader in log.get_relations()
                .map_err(|e| format!("get relations: {}", e))? {
                let rel = Relation::from_capnp(rel_reader)?;
                let existing_version = by_uuid.get(&rel.uuid)
                    .map(|r| r.version)
                    .unwrap_or(0);
                if rel.version >= existing_version {
                    by_uuid.insert(rel.uuid, rel);
                }
            }
        }

        self.relations = by_uuid.into_values()
            .filter(|r| !r.deleted)
            .collect();
        Ok(())
    }

    /// Find all duplicate keys: keys with multiple live UUIDs in the log.
    /// Returns a map from key → vec of all live Node versions (one per UUID).
    /// The "winner" in self.nodes is always one of them.
    pub fn find_duplicates(&self) -> Result<HashMap<String, Vec<Node>>, String> {
        let path = nodes_path();
        if !path.exists() { return Ok(HashMap::new()); }

        let file = fs::File::open(&path)
            .map_err(|e| format!("open {}: {}", path.display(), e))?;
        let mut reader = BufReader::new(file);

        // Track latest version of each UUID
        let mut by_uuid: HashMap<[u8; 16], Node> = HashMap::new();

        while let Ok(msg) = serialize::read_message(&mut reader, message::ReaderOptions::new()) {
            let log = msg.get_root::<memory_capnp::node_log::Reader>()
                .map_err(|e| format!("read node log: {}", e))?;
            for node_reader in log.get_nodes()
                .map_err(|e| format!("get nodes: {}", e))? {
                let node = Node::from_capnp(node_reader)?;
                let dominated = by_uuid.get(&node.uuid)
                    .map(|n| node.version >= n.version)
                    .unwrap_or(true);
                if dominated {
                    by_uuid.insert(node.uuid, node);
                }
            }
        }

        // Group live (non-deleted) nodes by key
        let mut by_key: HashMap<String, Vec<Node>> = HashMap::new();
        for node in by_uuid.into_values() {
            if !node.deleted {
                by_key.entry(node.key.clone()).or_default().push(node);
            }
        }

        // Keep only duplicates
        by_key.retain(|_, nodes| nodes.len() > 1);
        Ok(by_key)
    }

    /// Append nodes to the log file.
    /// Serializes to a Vec first, then does a single write() syscall
    /// so the append is atomic with O_APPEND even without flock.
    pub fn append_nodes(&mut self, nodes: &[Node]) -> Result<(), String> {
        let _lock = StoreLock::acquire()?;
        self.append_nodes_unlocked(nodes)
    }

    /// Append nodes without acquiring the lock. Caller must hold StoreLock.
    pub(crate) fn append_nodes_unlocked(&mut self, nodes: &[Node]) -> Result<(), String> {
        let mut msg = message::Builder::new_default();
        {
            let log = msg.init_root::<memory_capnp::node_log::Builder>();
            let mut list = log.init_nodes(nodes.len() as u32);
            for (i, node) in nodes.iter().enumerate() {
                node.to_capnp(list.reborrow().get(i as u32));
            }
        }
        let mut buf = Vec::new();
        serialize::write_message(&mut buf, &msg)
            .map_err(|e| format!("serialize nodes: {}", e))?;

        let path = nodes_path();
        let file = fs::OpenOptions::new()
            .create(true).append(true).open(&path)
            .map_err(|e| format!("open {}: {}", path.display(), e))?;
        use std::io::Write;
        (&file).write_all(&buf)
            .map_err(|e| format!("write nodes: {}", e))?;

        self.loaded_nodes_size = file.metadata().map(|m| m.len()).unwrap_or(0);
        Ok(())
    }

    /// Replay only new entries appended to the node log since we last loaded.
    /// Call under StoreLock to catch writes from concurrent processes.
    pub(crate) fn refresh_nodes(&mut self) -> Result<(), String> {
        let path = nodes_path();
        let current_size = fs::metadata(&path).map(|m| m.len()).unwrap_or(0);
        if current_size <= self.loaded_nodes_size {
            return Ok(()); // no new data
        }

        let file = fs::File::open(&path)
            .map_err(|e| format!("open {}: {}", path.display(), e))?;
        let mut reader = BufReader::new(file);
        reader.seek(std::io::SeekFrom::Start(self.loaded_nodes_size))
            .map_err(|e| format!("seek nodes log: {}", e))?;

        while let Ok(msg) = serialize::read_message(&mut reader, message::ReaderOptions::new()) {
            let log = msg.get_root::<memory_capnp::node_log::Reader>()
                .map_err(|e| format!("read node log delta: {}", e))?;
            for node_reader in log.get_nodes()
                .map_err(|e| format!("get nodes delta: {}", e))? {
                let node = Node::from_capnp(node_reader)?;
                let dominated = self.nodes.get(&node.key)
                    .map(|n| node.version >= n.version)
                    .unwrap_or(true);
                if dominated {
                    if node.deleted {
                        self.nodes.remove(&node.key);
                        self.uuid_to_key.remove(&node.uuid);
                    } else {
                        self.uuid_to_key.insert(node.uuid, node.key.clone());
                        self.nodes.insert(node.key.clone(), node);
                    }
                }
            }
        }

        self.loaded_nodes_size = current_size;
        Ok(())
    }

    /// Append relations to the log file.
    /// Single write() syscall for atomic O_APPEND.
    pub fn append_relations(&mut self, relations: &[Relation]) -> Result<(), String> {
        let _lock = StoreLock::acquire()?;
        self.append_relations_unlocked(relations)
    }

    /// Append relations without acquiring the lock. Caller must hold StoreLock.
    pub(crate) fn append_relations_unlocked(&mut self, relations: &[Relation]) -> Result<(), String> {
        let mut msg = message::Builder::new_default();
        {
            let log = msg.init_root::<memory_capnp::relation_log::Builder>();
            let mut list = log.init_relations(relations.len() as u32);
            for (i, rel) in relations.iter().enumerate() {
                rel.to_capnp(list.reborrow().get(i as u32));
            }
        }
        let mut buf = Vec::new();
        serialize::write_message(&mut buf, &msg)
            .map_err(|e| format!("serialize relations: {}", e))?;

        let path = relations_path();
        let file = fs::OpenOptions::new()
            .create(true).append(true).open(&path)
            .map_err(|e| format!("open {}: {}", path.display(), e))?;
        use std::io::Write;
        (&file).write_all(&buf)
            .map_err(|e| format!("write relations: {}", e))?;

        self.loaded_rels_size = file.metadata().map(|m| m.len()).unwrap_or(0);
        Ok(())
    }

    /// Append agent visit records to the visits log.
    pub fn append_visits(&mut self, visits: &[AgentVisit]) -> Result<(), String> {
        if visits.is_empty() { return Ok(()); }

        let mut msg = message::Builder::new_default();
        {
            let log = msg.init_root::<memory_capnp::agent_visit_log::Builder>();
            let mut list = log.init_visits(visits.len() as u32);
            for (i, visit) in visits.iter().enumerate() {
                visit.to_capnp(list.reborrow().get(i as u32));
            }
        }
        let mut buf = Vec::new();
        serialize::write_message(&mut buf, &msg)
            .map_err(|e| format!("serialize visits: {}", e))?;

        let path = visits_path();
        let file = fs::OpenOptions::new()
            .create(true).append(true).open(&path)
            .map_err(|e| format!("open {}: {}", path.display(), e))?;
        use std::io::Write;
        (&file).write_all(&buf)
            .map_err(|e| format!("write visits: {}", e))?;

        // Update in-memory index
        for v in visits {
            self.visits
                .entry(v.node_key.clone())
                .or_default()
                .insert(v.agent.clone(), v.timestamp);
        }

        Ok(())
    }

    /// Replay visits log to rebuild in-memory index.
    fn replay_visits(&mut self, path: &Path) -> Result<(), String> {
        let file = fs::File::open(path)
            .map_err(|e| format!("open {}: {}", path.display(), e))?;
        let mut reader = BufReader::new(file);

        while reader.stream_position().map_err(|e| e.to_string())?
              < fs::metadata(path).map_err(|e| e.to_string())?.len()
        {
            let msg = match serialize::read_message(&mut reader, Default::default()) {
                Ok(m) => m,
                Err(_) => break,
            };
            let log = msg.get_root::<memory_capnp::agent_visit_log::Reader>()
                .map_err(|e| format!("read visit log: {}", e))?;

            for visit in log.get_visits().map_err(|e| e.to_string())? {
                let key = visit.get_node_key().ok()
                    .and_then(|t| t.to_str().ok())
                    .unwrap_or("")
                    .to_string();
                let agent = visit.get_agent().ok()
                    .and_then(|t| t.to_str().ok())
                    .unwrap_or("")
                    .to_string();
                let ts = visit.get_timestamp();

                if !key.is_empty() && !agent.is_empty() {
                    let entry = self.visits.entry(key).or_default();
                    // Keep latest timestamp per agent
                    let existing = entry.entry(agent).or_insert(0);
                    if ts > *existing {
                        *existing = ts;
                    }
                }
            }
        }
        Ok(())
    }

    /// Record visits for a batch of node keys from a successful agent run.
    pub fn record_agent_visits(&mut self, node_keys: &[String], agent: &str) -> Result<(), String> {
        let visits: Vec<AgentVisit> = node_keys.iter()
            .filter_map(|key| {
                let node = self.nodes.get(key)?;
                Some(new_visit(node.uuid, key, agent, "processed"))
            })
            .collect();
        self.append_visits(&visits)
    }

    /// Get the last time an agent visited a node. Returns 0 if never visited.
    pub fn last_visited(&self, node_key: &str, agent: &str) -> i64 {
        self.visits.get(node_key)
            .and_then(|agents| agents.get(agent))
            .copied()
            .unwrap_or(0)
    }

    /// Save the derived cache with log size header for staleness detection.
    /// Uses atomic write (tmp + rename) to prevent partial reads.
    pub fn save(&self) -> Result<(), String> {
        let _lock = StoreLock::acquire()?;

        let path = state_path();
        if let Some(parent) = path.parent() {
            fs::create_dir_all(parent).ok();
        }

        // Use log sizes from load time, not current filesystem sizes.
        // If another writer appended since we loaded, our recorded size
        // will be smaller than the actual log → next reader detects stale
        // cache and replays the (correct, append-only) log.
        let nodes_size = self.loaded_nodes_size;
        let rels_size = self.loaded_rels_size;

        let bincode_data = bincode::serialize(self)
            .map_err(|e| format!("bincode serialize: {}", e))?;

        let mut data = Vec::with_capacity(CACHE_HEADER_LEN + bincode_data.len());
        data.extend_from_slice(&CACHE_MAGIC);
        data.extend_from_slice(&nodes_size.to_le_bytes());
        data.extend_from_slice(&rels_size.to_le_bytes());
        data.extend_from_slice(&bincode_data);

        // Atomic write: tmp file + rename
        let tmp_path = path.with_extension("bin.tmp");
        fs::write(&tmp_path, &data)
            .map_err(|e| format!("write {}: {}", tmp_path.display(), e))?;
        fs::rename(&tmp_path, &path)
            .map_err(|e| format!("rename {} → {}: {}", tmp_path.display(), path.display(), e))?;

        // Also write rkyv snapshot (mmap-friendly)
        if let Err(e) = self.save_snapshot(nodes_size, rels_size) {
            eprintln!("rkyv snapshot save: {}", e);
        }

        Ok(())
    }

    /// Serialize store as rkyv snapshot with staleness header.
    /// Assumes StoreLock is already held by caller.
    fn save_snapshot(&self, nodes_size: u64, rels_size: u64) -> Result<(), String> {
        let snap = Snapshot {
            nodes: self.nodes.clone(),
            relations: self.relations.iter().filter(|r| !r.deleted).cloned().collect(),
            gaps: self.gaps.clone(),
            params: self.params,
        };

        let rkyv_data = rkyv::to_bytes::<_, 256>(&snap)
            .map_err(|e| format!("rkyv serialize: {}", e))?;

        let mut data = Vec::with_capacity(RKYV_HEADER_LEN + rkyv_data.len());
        data.extend_from_slice(&RKYV_MAGIC);
        data.extend_from_slice(&1u32.to_le_bytes());  // format version
        data.extend_from_slice(&nodes_size.to_le_bytes());
        data.extend_from_slice(&rels_size.to_le_bytes());
        data.extend_from_slice(&(rkyv_data.len() as u64).to_le_bytes());
        data.extend_from_slice(&rkyv_data);

        let path = snapshot_path();
        let tmp_path = path.with_extension("rkyv.tmp");
        fs::write(&tmp_path, &data)
            .map_err(|e| format!("write {}: {}", tmp_path.display(), e))?;
        fs::rename(&tmp_path, &path)
            .map_err(|e| format!("rename: {}", e))?;

        Ok(())
    }

    /// Try loading store from mmap'd rkyv snapshot.
    /// Returns None if snapshot is missing or stale (log sizes don't match).
    fn load_snapshot_mmap() -> Result<Option<Store>, String> {
        let path = snapshot_path();
        if !path.exists() { return Ok(None); }

        let nodes_size = fs::metadata(nodes_path()).map(|m| m.len()).unwrap_or(0);
        let rels_size = fs::metadata(relations_path()).map(|m| m.len()).unwrap_or(0);

        let file = fs::File::open(&path)
            .map_err(|e| format!("open {}: {}", path.display(), e))?;

        let mmap = unsafe { memmap2::Mmap::map(&file) }
            .map_err(|e| format!("mmap {}: {}", path.display(), e))?;

        if mmap.len() < RKYV_HEADER_LEN { return Ok(None); }
        if mmap[..4] != RKYV_MAGIC { return Ok(None); }

        // [4..8] = version, skip for now
        let cached_nodes = u64::from_le_bytes(mmap[8..16].try_into().unwrap());
        let cached_rels = u64::from_le_bytes(mmap[16..24].try_into().unwrap());
        let data_len = u64::from_le_bytes(mmap[24..32].try_into().unwrap()) as usize;

        if cached_nodes != nodes_size || cached_rels != rels_size {
            return Ok(None); // stale
        }
        if mmap.len() < RKYV_HEADER_LEN + data_len {
            return Ok(None); // truncated
        }

        let rkyv_data = &mmap[RKYV_HEADER_LEN..RKYV_HEADER_LEN + data_len];

        // SAFETY: we wrote this file ourselves via save_snapshot().
        // Skip full validation (check_archived_root) — the staleness header
        // already confirms this snapshot matches the current log state.
        let archived = unsafe { rkyv::archived_root::<Snapshot>(rkyv_data) };

        let snap: Snapshot = <ArchivedSnapshot as rkyv::Deserialize<Snapshot, rkyv::Infallible>>
            ::deserialize(archived, &mut rkyv::Infallible).unwrap();

        let mut store = Store {
            nodes: snap.nodes,
            relations: snap.relations,
            gaps: snap.gaps,
            params: snap.params,
            ..Default::default()
        };

        // Rebuild uuid_to_key (not serialized)
        for (key, node) in &store.nodes {
            store.uuid_to_key.insert(node.uuid, key.clone());
        }
        store.loaded_nodes_size = nodes_size;
        store.loaded_rels_size = rels_size;

        Ok(Some(store))
    }
}

/// Strip .md suffix from all node keys and relation key strings.
/// Merges duplicates (bare key + .md key) by keeping the latest version.
pub fn strip_md_keys() -> Result<(), String> {
    use super::strip_md_suffix;

    let mut store = Store::load()?;
    let mut renamed_nodes = 0usize;
    let mut renamed_rels = 0usize;
    let mut merged = 0usize;

    // Collect keys that need renaming
    let old_keys: Vec<String> = store.nodes.keys()
        .filter(|k| k.ends_with(".md") || k.contains(".md#"))
        .cloned()
        .collect();

    for old_key in &old_keys {
        let new_key = strip_md_suffix(old_key);
        if new_key == *old_key { continue; }

        let mut node = store.nodes.remove(old_key).unwrap();
        store.uuid_to_key.remove(&node.uuid);

        if let Some(existing) = store.nodes.get(&new_key) {
            // Merge: keep whichever has the higher version
            if existing.version >= node.version {
                eprintln!("  merge {} → {} (keeping existing v{})",
                    old_key, new_key, existing.version);
                merged += 1;
                continue;
            }
            eprintln!("  merge {} → {} (replacing v{} with v{})",
                old_key, new_key, existing.version, node.version);
            merged += 1;
        }

        node.key = new_key.clone();
        node.version += 1;
        store.uuid_to_key.insert(node.uuid, new_key.clone());
        store.nodes.insert(new_key, node);
        renamed_nodes += 1;
    }

    // Fix relation key strings
    for rel in &mut store.relations {
        let new_source = strip_md_suffix(&rel.source_key);
        let new_target = strip_md_suffix(&rel.target_key);
        if new_source != rel.source_key || new_target != rel.target_key {
            rel.source_key = new_source;
            rel.target_key = new_target;
            rel.version += 1;
            renamed_rels += 1;
        }
    }

    if renamed_nodes == 0 && renamed_rels == 0 && merged == 0 {
        eprintln!("No .md suffixes found — store is clean");
        return Ok(());
    }

    eprintln!("Renamed {} nodes, {} relations, merged {} duplicates",
        renamed_nodes, renamed_rels, merged);

    // Write fresh logs from the migrated state
    rewrite_store(&store)?;

    eprintln!("Store rewritten successfully");
    Ok(())
}

/// Rewrite the entire store from scratch (fresh logs + caches).
/// Used after migrations that change keys across all nodes/relations.
fn rewrite_store(store: &Store) -> Result<(), String> {
    let _lock = StoreLock::acquire()?;

    // Write fresh node log
    let nodes: Vec<_> = store.nodes.values().cloned().collect();
    let nodes_path = nodes_path();
    {
        let file = fs::File::create(&nodes_path)
            .map_err(|e| format!("create {}: {}", nodes_path.display(), e))?;
        let mut writer = BufWriter::new(file);

        // Write in chunks to keep message sizes reasonable
        for chunk in nodes.chunks(100) {
            let mut msg = message::Builder::new_default();
            {
                let log = msg.init_root::<memory_capnp::node_log::Builder>();
                let mut list = log.init_nodes(chunk.len() as u32);
                for (i, node) in chunk.iter().enumerate() {
                    node.to_capnp(list.reborrow().get(i as u32));
                }
            }
            serialize::write_message(&mut writer, &msg)
                .map_err(|e| format!("write nodes: {}", e))?;
        }
    }

    // Write fresh relation log
    let rels_path = relations_path();
    {
        let file = fs::File::create(&rels_path)
            .map_err(|e| format!("create {}: {}", rels_path.display(), e))?;
        let mut writer = BufWriter::new(file);

        let rels: Vec<_> = store.relations.iter().filter(|r| !r.deleted).cloned().collect();
        if !rels.is_empty() {
            for chunk in rels.chunks(100) {
                let mut msg = message::Builder::new_default();
                {
                    let log = msg.init_root::<memory_capnp::relation_log::Builder>();
                    let mut list = log.init_relations(chunk.len() as u32);
                    for (i, rel) in chunk.iter().enumerate() {
                        rel.to_capnp(list.reborrow().get(i as u32));
                    }
                }
                serialize::write_message(&mut writer, &msg)
                    .map_err(|e| format!("write relations: {}", e))?;
            }
        }
    }

    // Nuke caches so next load rebuilds from fresh logs
    for p in [state_path(), snapshot_path()] {
        if p.exists() {
            fs::remove_file(&p).ok();
        }
    }

    Ok(())
}

/// Check and repair corrupt capnp log files.
///
/// Reads each message sequentially, tracking file position. On the first
/// corrupt message, truncates the file to the last good position. Also
/// removes stale caches so the next load replays from the repaired log.
pub fn fsck() -> Result<(), String> {
    let mut any_corrupt = false;

    for (path, kind) in [
        (nodes_path(), "node"),
        (relations_path(), "relation"),
    ] {
        if !path.exists() { continue; }

        let file = fs::File::open(&path)
            .map_err(|e| format!("open {}: {}", path.display(), e))?;
        let file_len = file.metadata()
            .map_err(|e| format!("stat {}: {}", path.display(), e))?.len();
        let mut reader = BufReader::new(file);

        let mut good_messages = 0u64;
        let mut last_good_pos = 0u64;

        loop {
            let pos = reader.stream_position()
                .map_err(|e| format!("tell {}: {}", path.display(), e))?;

            let msg = match serialize::read_message(&mut reader, message::ReaderOptions::new()) {
                Ok(m) => m,
                Err(_) => {
                    // read_message fails at EOF (normal) or on corrupt framing
                    if pos < file_len {
                        // Not at EOF — corrupt framing
                        eprintln!("{}: corrupt message at offset {}, truncating", kind, pos);
                        any_corrupt = true;
                        drop(reader);
                        let file = fs::OpenOptions::new().write(true).open(&path)
                            .map_err(|e| format!("open for truncate: {}", e))?;
                        file.set_len(pos)
                            .map_err(|e| format!("truncate {}: {}", path.display(), e))?;
                        eprintln!("{}: truncated from {} to {} bytes ({} good messages)",
                            kind, file_len, pos, good_messages);
                    }
                    break;
                }
            };

            // Validate the message content too
            let valid = if kind == "node" {
                msg.get_root::<memory_capnp::node_log::Reader>()
                    .and_then(|l| l.get_nodes().map(|_| ()))
                    .is_ok()
            } else {
                msg.get_root::<memory_capnp::relation_log::Reader>()
                    .and_then(|l| l.get_relations().map(|_| ()))
                    .is_ok()
            };

            if valid {
                good_messages += 1;
                last_good_pos = reader.stream_position()
                    .map_err(|e| format!("tell {}: {}", path.display(), e))?;
            } else {
                eprintln!("{}: corrupt message content at offset {}, truncating to {}",
                    kind, pos, last_good_pos);
                any_corrupt = true;
                drop(reader);
                let file = fs::OpenOptions::new().write(true).open(&path)
                    .map_err(|e| format!("open for truncate: {}", e))?;
                file.set_len(last_good_pos)
                    .map_err(|e| format!("truncate {}: {}", path.display(), e))?;
                eprintln!("{}: truncated from {} to {} bytes ({} good messages)",
                    kind, file_len, last_good_pos, good_messages);
                break;
            }
        }

        if !any_corrupt {
            eprintln!("{}: {} messages, all clean", kind, good_messages);
        }
    }

    if any_corrupt {
        // Nuke caches so next load replays from the repaired logs
        for p in [state_path(), snapshot_path()] {
            if p.exists() {
                fs::remove_file(&p)
                    .map_err(|e| format!("remove {}: {}", p.display(), e))?;
                eprintln!("removed stale cache: {}", p.display());
            }
        }
        eprintln!("repair complete — run `poc-memory status` to verify");
    } else {
        eprintln!("store is clean");
    }

    Ok(())
}