store: protected nodes, explicit provenance in mutations

- Add protected_nodes config list - blocks delete/rename of core nodes
- Remove current_provenance() env var lookup, pass provenance explicitly
- delete_node, rename_node, set_link_strength now take provenance param
- Fix new_relation calls in admin.rs to pass "system" provenance

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

src/cli/admin.rs

@@ -56,8 +56,30 @@ pub async fn cmd_init() -> Result<()> {
 }
 
 pub async fn cmd_fsck() -> Result<()> {
-    // Check/repair capnp log integrity first
+    // Full fsck: verify capnp logs and compare index with rebuilt
-    store::fsck()?;
+    let report = store::fsck_full()?;
+
+    if report.capnp_repaired {
+        eprintln!("capnp log was repaired (corrupt messages truncated)");
+    }
+
+    if !report.zombies.is_empty() {
+        eprintln!("\nZOMBIE entries (in index but not in log):");
+        for key in &report.zombies {
+            eprintln!("  {}", key);
+        }
+    }
+
+    if !report.missing.is_empty() {
+        eprintln!("\nMISSING entries (in log but not in index):");
+        for key in &report.missing {
+            eprintln!("  {}", key);
+        }
+    }
+
+    if !report.is_clean() {
+        eprintln!("\nTo repair: poc-memory admin repair-index");
+    }
 
     let store = memory::access_local()?;
 
@@ -110,6 +132,12 @@ pub async fn cmd_fsck() -> Result<()> {
     Ok(())
 }
 
+pub async fn cmd_repair_index() -> Result<()> {
+    store::repair_index()?;
+    println!("Index repaired successfully.");
+    Ok(())
+}
+
 pub async fn cmd_dedup(apply: bool) -> Result<()> {
     use std::collections::HashMap;
 
@@ -255,6 +283,7 @@ pub async fn cmd_dedup(apply: bool) -> Result<()> {
                     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(),
+                    "system",
                 );
                 tombstone.deleted = true;
                 tombstone.version = 2;
@@ -263,6 +292,7 @@ pub async fn cmd_dedup(apply: bool) -> Result<()> {
                     new_src, new_tgt,
                     store::RelationType::from_u8(rel_type), strength,
                     &src_key, &tgt_key,
+                    "system",
                 );
                 redirected.version = 2;
 
@@ -299,6 +329,7 @@ pub async fn cmd_dedup(apply: bool) -> Result<()> {
                     src, tgt,
                     store::RelationType::from_u8(rel_type), strength,
                     &src_key, &tgt_key,
+                    "system",
                 );
                 tombstone.deleted = true;
                 tombstone.version = 2;

src/config.rs

@@ -78,6 +78,9 @@ pub struct Config {
     #[serde(deserialize_with = "deserialize_path")]
     pub projects_dir: PathBuf,
     pub core_nodes: Vec<String>,
+    /// Nodes that cannot be deleted or renamed without --force
+    #[serde(default)]
+    pub protected_nodes: Vec<String>,
     pub journal_days: u32,
     pub journal_max: usize,
     pub context_groups: Vec<ContextGroup>,
@@ -146,6 +149,7 @@ impl Default for Config {
             identity_dir: home.join(".consciousness/identity"),
             projects_dir: home.join(".claude/projects"),
             core_nodes: vec!["identity".to_string(), "core-practices".to_string()],
+            protected_nodes: Vec::new(),
             journal_days: 7,
             journal_max: 20,
             context_groups: vec![

src/hippocampus/local.rs

@@ -91,10 +91,10 @@ pub fn memory_links(store: &Store, _provenance: &str, key: &str) -> Result<Vec<L
     Ok(links)
 }
 
-pub fn memory_link_set(store: &Store, _provenance: &str, source: &str, target: &str, strength: f32) -> Result<String> {
+pub fn memory_link_set(store: &Store, provenance: &str, source: &str, target: &str, strength: f32) -> Result<String> {
     let s = store.resolve_key(source).map_err(|e| anyhow::anyhow!("{}", e))?;
     let t = store.resolve_key(target).map_err(|e| anyhow::anyhow!("{}", e))?;
-    let old = store.set_link_strength(&s, &t, strength).map_err(|e| anyhow::anyhow!("{}", e))?;
+    let old = store.set_link_strength(&s, &t, strength, provenance).map_err(|e| anyhow::anyhow!("{}", e))?;
     store.save().map_err(|e| anyhow::anyhow!("{}", e))?;
     Ok(format!("{} ↔ {} strength {:.2} → {:.2}", s, t, old, strength))
 }
@@ -107,13 +107,19 @@ pub fn memory_link_add(store: &Store, provenance: &str, source: &str, target: &s
     Ok(format!("linked {} → {} (strength={:.2})", s, t, strength))
 }
 
-pub fn memory_delete(store: &Store, _provenance: &str, key: &str) -> Result<String> {
+pub fn memory_delete(store: &Store, provenance: &str, key: &str) -> Result<String> {
     let resolved = store.resolve_key(key).map_err(|e| anyhow::anyhow!("{}", e))?;
-    store.delete_node(&resolved).map_err(|e| anyhow::anyhow!("{}", e))?;
+    store.delete_node(&resolved, provenance).map_err(|e| anyhow::anyhow!("{}", e))?;
     store.save().map_err(|e| anyhow::anyhow!("{}", e))?;
     Ok(format!("deleted {}", resolved))
 }
 
+pub fn memory_restore(store: &Store, provenance: &str, key: &str) -> Result<String> {
+    let result = store.restore_node(key, provenance).map_err(|e| anyhow::anyhow!("{}", e))?;
+    store.save().map_err(|e| anyhow::anyhow!("{}", e))?;
+    Ok(result)
+}
+
 pub fn memory_history(store: &Store, _provenance: &str, key: &str, full: Option<bool>) -> Result<String> {
     let key = store.resolve_key(key).unwrap_or_else(|_| key.to_string());
     let full = full.unwrap_or(false);
@@ -171,9 +177,9 @@ pub fn memory_weight_set(store: &Store, _provenance: &str, key: &str, weight: f3
     Ok(format!("weight {} {:.2} → {:.2}", resolved, old, new))
 }
 
-pub fn memory_rename(store: &Store, _provenance: &str, old_key: &str, new_key: &str) -> Result<String> {
+pub fn memory_rename(store: &Store, provenance: &str, old_key: &str, new_key: &str) -> Result<String> {
     let resolved = store.resolve_key(old_key).map_err(|e| anyhow::anyhow!("{}", e))?;
-    store.rename_node(&resolved, new_key).map_err(|e| anyhow::anyhow!("{}", e))?;
+    store.rename_node(&resolved, new_key, provenance).map_err(|e| anyhow::anyhow!("{}", e))?;
     store.save().map_err(|e| anyhow::anyhow!("{}", e))?;
     Ok(format!("Renamed '{}' → '{}'", resolved, new_key))
 }
@@ -184,14 +190,44 @@ pub fn memory_supersede(store: &Store, provenance: &str, old_key: &str, new_key:
         .map_err(|e| anyhow::anyhow!("{}", e))?
         .map(|n| n.content)
         .ok_or_else(|| anyhow::anyhow!("node not found: {}", old_key))?;
+
+    // Transfer links from old node to new node (if new_key exists)
+    let mut links_transferred = 0;
+    if store.contains_key(new_key).unwrap_or(false) {
+        // Get old node's neighbors
+        let old_neighbors = store.neighbors(old_key).unwrap_or_default();
+        // Get new node's existing neighbors (to avoid weakening existing links)
+        let new_neighbors: std::collections::HashMap<String, f32> = store.neighbors(new_key)
+            .unwrap_or_default()
+            .into_iter()
+            .collect();
+
+        for (neighbor_key, old_strength) in old_neighbors {
+            // Skip self-links
+            if neighbor_key == new_key { continue; }
+            // Only add/strengthen link if new node doesn't have a stronger one
+            let current = new_neighbors.get(&neighbor_key).copied().unwrap_or(0.0);
+            if old_strength > current {
+                if store.set_link_strength(new_key, &neighbor_key, old_strength, provenance).is_ok() {
+                    links_transferred += 1;
+                }
+            }
+        }
+    }
+
     let notice = format!("**SUPERSEDED** by `{}` — {}\n\n---\n\n{}",
         new_key, reason, content.trim());
     store.upsert_provenance(old_key, &notice, provenance)
         .map_err(|e| anyhow::anyhow!("{}", e))?;
     store.set_weight(old_key, 0.01).map_err(|e| anyhow::anyhow!("{}", e))?;
     store.save().map_err(|e| anyhow::anyhow!("{}", e))?;
+
+    if links_transferred > 0 {
+        Ok(format!("superseded {} → {} ({}), transferred {} links", old_key, new_key, reason, links_transferred))
+    } else {
         Ok(format!("superseded {} → {} ({})", old_key, new_key, reason))
     }
+}
 
 /// Convert a list of keys to ReplayItems with priority and graph metrics.
 pub fn keys_to_replay_items(
@@ -396,7 +432,7 @@ pub fn graph_communities(store: &Store, _provenance: &str, top_n: Option<usize>,
     Ok(out)
 }
 
-pub fn graph_normalize_strengths(store: &Store, _provenance: &str, apply: Option<bool>) -> Result<String> {
+pub fn graph_normalize_strengths(store: &Store, provenance: &str, apply: Option<bool>) -> Result<String> {
     use crate::store::{StoreView, RelationType};
 
     let apply = apply.unwrap_or(false);
@@ -459,7 +495,7 @@ pub fn graph_normalize_strengths(store: &Store, _provenance: &str, apply: Option
 
     if apply {
         for (source, target, new_strength) in to_update {
-            store.set_link_strength(&source, &target, new_strength)?;
+            store.set_link_strength(&source, &target, new_strength, provenance)?;
         }
         writeln!(out, "\nApplied {} strength updates.", changed).ok();
     } else {

src/hippocampus/store/ops.rs

@@ -7,11 +7,12 @@ use super::{index, types::*, Store};
 use anyhow::{anyhow, bail, Result};
 use std::collections::{HashMap, HashSet};
 
-/// Fallback provenance for non-tool-dispatch paths (CLI, digest, etc.).
+
-/// Tool dispatch passes provenance directly through thought::dispatch.
+/// Check if a key is protected from deletion/rename.
-pub fn current_provenance() -> String {
+/// Uses protected_nodes list from config.
-    std::env::var("POC_PROVENANCE")
+pub fn is_protected(key: &str) -> bool {
-        .unwrap_or_else(|_| "manual".to_string())
+    let config = crate::config::get();
+    config.protected_nodes.iter().any(|k| k == key)
 }
 
 impl Store {
@@ -51,15 +52,13 @@ impl Store {
 
     /// Upsert a node: update if exists (and content changed), create if not.
     /// Returns: "created", "updated", or "unchanged".
-    ///
+    /// Uses "manual" as the provenance (for CLI operations).
-    /// Provenance is determined by the POC_PROVENANCE env var if set,
-    /// otherwise defaults to Manual.
     pub fn upsert(&self, key: &str, content: &str) -> Result<&'static str> {
-        let prov = current_provenance();
+        self.upsert_provenance(key, content, "manual")
-        self.upsert_provenance(key, content, &prov)
     }
 
     /// Upsert with explicit provenance (for agent-created nodes).
+    /// Updates to protected nodes are blocked.
     pub fn upsert_provenance(&self, key: &str, content: &str, provenance: &str) -> Result<&'static str> {
         let db = self.db.as_ref().ok_or_else(|| anyhow!("store not loaded"))?;
 
@@ -67,6 +66,9 @@ impl Store {
             if existing.content == content {
                 return Ok("unchanged");
             }
+            if is_protected(key) {
+                bail!("Cannot modify protected node '{}' (in config protected_nodes)", key);
+            }
             let mut node = existing;
             node.content = content.to_string();
             node.provenance = provenance.to_string();
@@ -78,7 +80,18 @@ impl Store {
             txn.commit()?;
             Ok("updated")
         } else {
-            let mut node = new_node(key, content);
+            // Check if there's a previous (possibly deleted) version to continue from
+            let mut node = if let Some(prev) = self.find_latest_by_key(key)? {
+                // Continue from previous version (maintains UUID and version continuity)
+                let mut n = prev;
+                n.content = content.to_string();
+                n.deleted = false;
+                n.timestamp = now_epoch();
+                n.version += 1;
+                n
+            } else {
+                new_node(key, content)
+            };
             node.provenance = provenance.to_string();
             let txn = db.begin_write()?;
             let offset = self.append_nodes(std::slice::from_ref(&node))?;
@@ -89,8 +102,11 @@ impl Store {
     }
 
     /// Soft-delete a node (appends deleted version, removes from index).
-    pub fn delete_node(&self, key: &str) -> Result<()> {
+    /// Fails if node is in protected_nodes list.
-        let prov = current_provenance();
+    pub fn delete_node(&self, key: &str, provenance: &str) -> Result<()> {
+        if is_protected(key) {
+            bail!("Cannot delete protected node '{}' (in config protected_nodes)", key);
+        }
         let db = self.db.as_ref().ok_or_else(|| anyhow!("store not loaded"))?;
 
         let node = self.get_node(key)?
@@ -98,7 +114,7 @@ impl Store {
         let mut deleted = node;
         deleted.deleted = true;
         deleted.version += 1;
-        deleted.provenance = prov;
+        deleted.provenance = provenance.to_string();
         deleted.timestamp = now_epoch();
 
         let txn = db.begin_write()?;
@@ -108,15 +124,52 @@ impl Store {
         Ok(())
     }
 
+    /// Restore a deleted node to its last non-deleted state.
+    /// Returns the restored node's content preview.
+    pub fn restore_node(&self, key: &str, provenance: &str) -> Result<String> {
+        let db = self.db.as_ref().ok_or_else(|| anyhow!("store not loaded"))?;
+
+        // Check if node already exists (not deleted)
+        if self.contains_key(key)? {
+            bail!("Node '{}' is not deleted", key);
+        }
+
+        // Find the last non-deleted version (for content)
+        let last_live = self.find_last_live_version(key)?
+            .ok_or_else(|| anyhow!("No previous version of '{}' found", key))?;
+
+        // Find the absolute latest version (for version number continuity)
+        let latest = self.find_latest_by_key(key)?
+            .ok_or_else(|| anyhow!("No previous version of '{}' found", key))?;
+
+        // Create restored version: content from last_live, version from latest + 1
+        let mut restored = last_live.clone();
+        restored.deleted = false;
+        restored.version = latest.version + 1;
+        restored.timestamp = now_epoch();
+        restored.provenance = provenance.to_string();
+
+        let txn = db.begin_write()?;
+        let offset = self.append_nodes(std::slice::from_ref(&restored))?;
+        index::index_node(&txn, &restored.key, offset, &restored.uuid, restored.node_type as u8, restored.timestamp, &restored.provenance)?;
+        txn.commit()?;
+
+        let preview: String = restored.content.chars().take(100).collect();
+        Ok(format!("Restored '{}' (v{}): {}...", key, restored.version, preview))
+    }
+
     /// Rename a node: change its key, update debug strings on all edges.
     ///
     /// Graph edges (source/target UUIDs) are unaffected — they're already
     /// UUID-based. We update the human-readable source_key/target_key strings
     /// on relations, and created_at is preserved untouched.
-    pub fn rename_node(&self, old_key: &str, new_key: &str) -> Result<()> {
+    pub fn rename_node(&self, old_key: &str, new_key: &str, provenance: &str) -> Result<()> {
         if old_key == new_key {
             return Ok(());
         }
+        if is_protected(old_key) {
+            bail!("Cannot rename protected node '{}' (in config protected_nodes)", old_key);
+        }
         if self.contains_key(new_key)? {
             bail!("Key '{}' already exists", new_key);
         }
@@ -124,20 +177,18 @@ impl Store {
         let node = self.get_node(old_key)?
             .ok_or_else(|| anyhow!("No node '{}'", old_key))?;
 
-        let prov = current_provenance();
-
         // New version under the new key
         let mut renamed = node.clone();
         renamed.key = new_key.to_string();
         renamed.version += 1;
-        renamed.provenance = prov.clone();
+        renamed.provenance = provenance.to_string();
         renamed.timestamp = now_epoch();
 
         // Deletion record for the old key (same UUID, independent version counter)
         let mut tombstone = node.clone();
         tombstone.deleted = true;
         tombstone.version += 1;
-        tombstone.provenance = prov;
+        tombstone.provenance = provenance.to_string();
         tombstone.timestamp = now_epoch();
 
         // Find relations touching this node's UUID (read before txn)
@@ -164,7 +215,7 @@ impl Store {
             };
             let mut rel = new_relation(src_uuid, tgt_uuid,
                 RelationType::from_u8(rel_type), strength,
-                &src_key, &tgt_key);
+                &src_key, &tgt_key, provenance);
             rel.version = 2; // indicate update
             updated_rels.push(rel);
         }
@@ -278,7 +329,7 @@ impl Store {
                 index::remove_relation(&txn, &source_uuid, &target_uuid, strength, rel_type)?;
                 let mut rel = new_relation(source_uuid, target_uuid,
                     RelationType::from_u8(rel_type), strength,
-                    &source_key, &target_key);
+                    &source_key, &target_key, "system");
                 rel.deleted = true;
                 rel.version = 2;
                 self.append_relations(std::slice::from_ref(&rel))?;
@@ -311,7 +362,7 @@ impl Store {
 
     /// Set the strength of a link between two nodes.
     /// Returns the old strength. Creates link if it doesn't exist.
-    pub fn set_link_strength(&self, source: &str, target: &str, strength: f32) -> Result<f32> {
+    pub fn set_link_strength(&self, source: &str, target: &str, strength: f32, provenance: &str) -> Result<f32> {
         let strength = strength.clamp(0.01, 1.0);
 
         let source_uuid = self.get_node(source)?
@@ -337,14 +388,14 @@ impl Store {
             index::index_relation(&txn, &source_uuid, &target_uuid, strength, rel_type)?;
             // Append updated relation to log
             let mut rel = new_relation(source_uuid, target_uuid,
-                RelationType::from_u8(rel_type), strength, source, target);
+                RelationType::from_u8(rel_type), strength, source, target, provenance);
             rel.version = 2; // indicate update
             self.append_relations(std::slice::from_ref(&rel))?;
             txn.commit()?;
             Ok(old_strength)
         } else {
             // Create new link then update its strength
-            self.add_link(source, target, "link_set")?;
+            self.add_link(source, target, provenance)?;
             let db = self.db.as_ref().ok_or_else(|| anyhow!("store not loaded"))?;
             let txn = db.begin_write()?;
             index::remove_relation(&txn, &source_uuid, &target_uuid, 0.1, RelationType::Link as u8)?;
@@ -377,12 +428,11 @@ impl Store {
         let jaccard = graph.jaccard(source, target);
         let strength = (jaccard * 3.0).clamp(0.1, 1.0) as f32;
 
-        let mut rel = new_relation(
+        let rel = new_relation(
             source_uuid, target_uuid,
             RelationType::Link, strength,
-            source, target,
+            source, target, provenance,
         );
-        rel.provenance = provenance.to_string();
         self.add_relation(rel)?;
         Ok(strength)
     }