fix: metadata-only update() never rewrites the noun record — the unconditional whole-vector save turned per-entity stat touches into full rewrites+fsync, amplifying read-heavy sweeps into disk saturation on a production deployment

Also: idle PathResolver stats tick no longer logs NaN% every minute (logs
only on new traffic, via prodLog); graph-lsm-* key family recognized as
system resources (kills the per-boot unknown-key warning on provider-backed
brains). Four regression pins in tests/integration/update-write-granularity.

src/brainy.ts

@@ -3161,18 +3161,23 @@ export class Brainy<T = any> implements BrainyInterface<T> {
           new UpdateNounMetadataOperation(this.storage, params.id, updatedMetadata)
         )
 
-        // Operation 2: Update vector data (will use updated type cache)
-        tx.addOperation(
-          new SaveNounOperation(this.storage, {
-            id: params.id,
-            vector,
-            connections: new Map(),
-            level: 0
-          })
-        )
-
-        // Operation 3-4: Update HNSW index (remove and re-add if reindexing needed)
+        // Operations 2-4: vector-record write + HNSW reindex — ONLY when the
+        // vector side actually changed (new data/vector/type). A metadata-only
+        // update must never rewrite the noun record: the record carries the
+        // full vector, so an unconditional save turned every metadata touch
+        // into a whole-vector rewrite + fsync — under a read-heavy consumer
+        // sweep that bumps per-entity stats, this amplified into disk
+        // saturation on a production deployment (SELF-ENGINE-RESTART-GRIND,
+        // 2026-07-29: 5.8GB written in 40min from ~50 recalls/min).
         if (needsReindexing) {
+          tx.addOperation(
+            new SaveNounOperation(this.storage, {
+              id: params.id,
+              vector,
+              connections: new Map(),
+              level: 0
+            })
+          )
           tx.addOperation(
             new RemoveFromVectorIndexOperation(this.index, params.id, existing.vector)
           )

src/storage/baseStorage.ts

@@ -382,6 +382,10 @@ export abstract class BaseStorage extends BaseStorageAdapter {
                                          // identical to the unknown-key fallback these keys hit
                                          // before being listed here — this only kills the
                                          // per-boot "Unknown key format" warning)
+      id.startsWith('graph-lsm-') ||     // Graph-LSM store manifests written through storage by
+                                         // an active native graph provider — same
+                                         // warn-then-route fallback as above; listing the family
+                                         // silences the per-boot warning on provider-backed brains
       isSingletonSystemKey(id)           // Known singletons (e.g. brainy:entityIdMapper) hit the
                                          // same warn-then-route fallback without this — the
                                          // routing below already handles them identically

src/vfs/PathResolver.ts

@@ -57,6 +57,7 @@ export class PathResolver {
   // Statistics
   private cacheHits = 0
   private cacheMisses = 0
+  private lastLoggedLookups = 0 // last total the maintenance tick logged stats at
   private metadataIndexHits = 0
   private metadataIndexMisses = 0
   private graphTraversalFallbacks = 0
@@ -519,10 +520,14 @@ export class PathResolver {
         }
       }
 
-      // Log cache statistics (in production, send to monitoring)
-      const hitRate = this.cacheHits / (this.cacheHits + this.cacheMisses)
-      if ((this.cacheHits + this.cacheMisses) % 1000 === 0) {
-        console.log(`[PathResolver] Cache stats: ${Math.round(hitRate * 100)}% hit rate, ${this.pathCache.size} entries, ${this.hotPaths.size} hot paths`)
+      // Log cache statistics only when there is new traffic to report — an
+      // idle resolver stays silent. 0/0 lookups previously rendered
+      // "NaN% hit rate" (and the %1000 gate passes at zero), which spammed
+      // production journals once a minute on every idle VFS.
+      const totalLookups = this.cacheHits + this.cacheMisses
+      if (totalLookups > 0 && totalLookups !== this.lastLoggedLookups && totalLookups % 1000 === 0) {
+        this.lastLoggedLookups = totalLookups
+        prodLog.debug(`[PathResolver] Cache stats: ${Math.round((this.cacheHits / totalLookups) * 100)}% hit rate, ${this.pathCache.size} entries, ${this.hotPaths.size} hot paths`)
       }
     }, 60000)  // Every minute
     // Cache maintenance must never keep the host process alive.