store: remove nodes and uuid_to_key HashMaps

All node access now goes through index → capnp:
- scoring.rs: consolidation_priority, replay_queue, consolidation_plan
- admin.rs: cmd_init, cmd_fsck, cmd_dedup
- engine.rs: run_generator, eval_filter, run_transform
- parser.rs: resolve_field, execute_query

Added Store::remove_from_index() for dedup cleanup.

The relations Vec remains for now (used for graph building).

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

src/hippocampus/store/mod.rs

@@ -32,7 +32,6 @@ pub use ops::current_provenance;
 
 use crate::graph::{self, Graph};
 
-use std::collections::HashMap;
 use anyhow::{bail, Result};
 
 /// Strip .md suffix from a key, handling both bare keys and section keys.
@@ -48,8 +47,6 @@ pub fn strip_md_suffix(key: &str) -> String {
 
 // The full in-memory store
 pub struct Store {
-    pub nodes: HashMap<String, Node>,          // key → latest node
-    pub uuid_to_key: HashMap<[u8; 16], String>, // uuid → key (rebuilt from nodes)
     pub relations: Vec<Relation>,              // all active relations
     /// Log sizes at load time — used for staleness detection.
     pub(crate) loaded_nodes_size: u64,
@@ -61,8 +58,6 @@ pub struct Store {
 impl Default for Store {
     fn default() -> Self {
         Store {
-            nodes: HashMap::new(),
-            uuid_to_key: HashMap::new(),
             relations: Vec::new(),
             loaded_nodes_size: 0,
             loaded_rels_size: 0,
@@ -101,6 +96,14 @@ impl Store {
         index::all_keys(db)
     }
 
+    /// 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)?;
+        }
+        Ok(())
+    }
+
     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);