fix: use runCommandWithCheck for database commands

Author: Crushdada

src/tools/mongodb/delete/deleteMany.ts

@@ -28,7 +28,7 @@ export class DeleteManyTool extends MongoDBToolBase {
         // Check if delete operation uses an index if enabled
         if (this.config.indexCheck) {
             await checkIndexUsage(provider, database, collection, "deleteMany", async () => {
-                return provider.mongoClient.db(database).command({
+                return provider.runCommandWithCheck(database, {
                     explain: {
                         delete: collection,
                         deletes: [

src/tools/mongodb/metadata/explain.ts

@@ -76,7 +76,7 @@ export class ExplainTool extends MongoDBToolBase {
             }
             case "count": {
                 const { query } = method.arguments;
-                result = await provider.mongoClient.db(database).command({
+                result = await provider.runCommandWithCheck(database, {
                     explain: {
                         count: collection,
                         query,

src/tools/mongodb/read/count.ts

@@ -30,7 +30,7 @@ export class CountTool extends MongoDBToolBase {
         // Check if count operation uses an index if enabled
         if (this.config.indexCheck) {
             await checkIndexUsage(provider, database, collection, "count", async () => {
-                return provider.mongoClient.db(database).command({
+                return provider.runCommandWithCheck(database, {
                     explain: {
                         count: collection,
                         query,

src/tools/mongodb/update/updateMany.ts

@@ -37,7 +37,7 @@ export class UpdateManyTool extends MongoDBToolBase {
         // Check if update operation uses an index if enabled
         if (this.config.indexCheck) {
             await checkIndexUsage(provider, database, collection, "updateMany", async () => {
-                return provider.mongoClient.db(database).command({
+                return provider.runCommandWithCheck(database, {
                     explain: {
                         update: collection,
                         updates: [