diff --git a/src/importers/VFSStructureGenerator.ts b/src/importers/VFSStructureGenerator.ts
index 46b74cf5..e638d747 100644
--- a/src/importers/VFSStructureGenerator.ts
+++ b/src/importers/VFSStructureGenerator.ts
@@ -189,8 +189,7 @@ export class VFSStructureGenerator {
       reportProgress('metadata', `Preserved source file: ${options.sourceFilename}`)
     }
 
-    // Note: groups already calculated above for progress tracking
-    // const groups = this.groupEntities(importResult, options)
+    // `groups` was already computed above (for progress tracking) and is reused here.
 
     // Create directories and files for each group
     for (const [groupName, entities] of groups.entries()) {
diff --git a/src/storage/adapters/fileSystemStorage.ts b/src/storage/adapters/fileSystemStorage.ts
index 3f8f5118..fdca6e13 100644
--- a/src/storage/adapters/fileSystemStorage.ts
+++ b/src/storage/adapters/fileSystemStorage.ts
@@ -661,35 +661,6 @@ export class FileSystemStorage extends BaseStorage {
     return allEdges
   }
 
-  /**
-   * Get edges by source
-   */
-  protected async getEdgesBySource(sourceId: string): Promise<Edge[]> {
-    // This method is deprecated and would require loading metadata for each edge
-    // For now, return empty array since this is not efficiently implementable with new storage pattern
-    console.warn('getEdgesBySource is deprecated and not efficiently supported in new storage pattern')
-    return []
-  }
-
-  /**
-   * Get edges by target
-   */
-  protected async getEdgesByTarget(targetId: string): Promise<Edge[]> {
-    // This method is deprecated and would require loading metadata for each edge
-    // For now, return empty array since this is not efficiently implementable with new storage pattern
-    console.warn('getEdgesByTarget is deprecated and not efficiently supported in new storage pattern')
-    return []
-  }
-
-  /**
-   * Get edges by type
-   */
-  protected async getEdgesByType(type: string): Promise<Edge[]> {
-    // This method is deprecated and would require loading metadata for each edge
-    // For now, return empty array since this is not efficiently implementable with new storage pattern
-    console.warn('getEdgesByType is deprecated and not efficiently supported in new storage pattern')
-    return []
-  }
 
   /**
    * Delete an edge from storage
diff --git a/src/utils/metadataIndex.ts b/src/utils/metadataIndex.ts
index 31fca200..59259150 100644
--- a/src/utils/metadataIndex.ts
+++ b/src/utils/metadataIndex.ts
@@ -2311,81 +2311,6 @@ export class MetadataIndexManager implements MetadataIndexProvider {
     return normalized
   }
 
-  /**
-   * DEPRECATED - Old implementation for backward compatibility
-   */
-  private async getIdsForFilterOld(filter: any): Promise<string[]> {
-    if (!filter || Object.keys(filter).length === 0) {
-      return []
-    }
-    
-    // Handle logical operators
-    if (filter.allOf && Array.isArray(filter.allOf)) {
-      // For allOf, we need intersection of all sub-filters
-      const allIds: string[][] = []
-      for (const subFilter of filter.allOf) {
-        const subIds = await this.getIdsForFilter(subFilter)
-        allIds.push(subIds)
-      }
-      
-      if (allIds.length === 0) return []
-      if (allIds.length === 1) return allIds[0]
-      
-      // Intersection of all sets
-      return allIds.reduce((intersection, currentSet) => 
-        intersection.filter(id => currentSet.includes(id))
-      )
-    }
-    
-    if (filter.anyOf && Array.isArray(filter.anyOf)) {
-      // For anyOf, we need union of all sub-filters
-      const unionIds = new Set<string>()
-      for (const subFilter of filter.anyOf) {
-        const subIds = await this.getIdsForFilter(subFilter)
-        subIds.forEach(id => unionIds.add(id))
-      }
-      return Array.from(unionIds)
-    }
-    
-    // Handle regular field filters
-    const criteria = this.convertFilterToCriteria(filter)
-    const idSets: string[][] = []
-    const unindexedFields: string[] = []
-
-    for (const { field, values } of criteria) {
-      const unionIds = new Set<string>()
-      try {
-        for (const value of values) {
-          const ids = await this.getIds(field, value)
-          ids.forEach(id => unionIds.add(id))
-        }
-      } catch (err) {
-        if (err instanceof BrainyError && err.type === 'FIELD_NOT_INDEXED') {
-          unindexedFields.push(field)
-          // Treat as no matches and continue — same semantics as the main
-          // getIdsForFilter() path.
-        } else {
-          throw err
-        }
-      }
-      idSets.push(Array.from(unionIds))
-    }
-
-    if (unindexedFields.length > 0) {
-      prodLog.warn(
-        `[brainy] find() where-clause referenced unindexed field(s) ` +
-        `${unindexedFields.join(', ')}; their clauses contributed no rows.`
-      )
-    }
-    if (idSets.length === 0) return []
-    if (idSets.length === 1) return idSets[0]
-
-    // Intersection of all field criteria (implicit $and)
-    return idSets.reduce((intersection, currentSet) =>
-      intersection.filter(id => currentSet.includes(id))
-    )
-  }
-
   /**
    * Flush dirty entries to storage (non-blocking version)
    * NOTE: Sparse indices are flushed immediately in add/remove operations