user provided serialization fixes for dml-tools property

Author: souvikghosh04

src/Cli.Tests/ConfigGeneratorTests.cs

@@ -165,15 +165,7 @@ public void TestSpecialCharactersInConnectionString()
                  },
                  ""mcp"": {
                  ""enabled"": true,
-                 ""path"": ""/mcp"",
-                 ""dml-tools"":{
-                   ""describe-entities"": true,
-                   ""create-record"": true,
-                   ""read-records"": true,
-                   ""update-record"": true,
-                   ""delete-record"": true,
-                   ""execute-entity"":true
-                 }
+                 ""path"": ""/mcp""
                 },
                 ""host"": {
                   ""cors"": {

src/Config/Converters/DmlToolsConfigConverter.cs

@@ -139,12 +139,13 @@ public override void Write(Utf8JsonWriter writer, DmlToolsConfig? value, JsonSer
 
         // Only write the boolean value if it's provided by user
         // This prevents writing "dml-tools": true when it's the default
-        if (!hasIndividualSettings && value.UserProvidedAllToolsEnabled)
+        if (!hasIndividualSettings && value.UserProvidedAllTools)
         {
             writer.WritePropertyName("dml-tools");
             writer.WriteBooleanValue(value.AllToolsEnabled);
         }
-        else
+
+        if(hasIndividualSettings)
         {
             writer.WritePropertyName("dml-tools");
 

src/Config/ObjectModel/DmlToolsConfig.cs

@@ -64,61 +64,79 @@ public DmlToolsConfig(
         if (allToolsEnabled is not null)
         {
             AllToolsEnabled = allToolsEnabled.Value;
-            UserProvidedAllToolsEnabled = true;
+            UserProvidedAllTools = true;
+
+            // When allToolsEnabled is set, use it as the default for all tools
+            bool toolDefault = allToolsEnabled.Value;
+
+            DescribeEntities = describeEntities ?? toolDefault;
+            CreateRecord = createRecord ?? toolDefault;
+            ReadRecords = readRecords ?? toolDefault;
+            UpdateRecord = updateRecord ?? toolDefault;
+            DeleteRecord = deleteRecord ?? toolDefault;
+            ExecuteEntity = executeEntity ?? toolDefault;
         }
         else
         {
             AllToolsEnabled = DEFAULT_ENABLED;
+
+            // Set values with defaults
+            DescribeEntities = describeEntities ?? DEFAULT_ENABLED;
+            CreateRecord = createRecord ?? DEFAULT_ENABLED;
+            ReadRecords = readRecords ?? DEFAULT_ENABLED;
+            UpdateRecord = updateRecord ?? DEFAULT_ENABLED;
+            DeleteRecord = deleteRecord ?? DEFAULT_ENABLED;
+            ExecuteEntity = executeEntity ?? DEFAULT_ENABLED;
         }
 
-        // Set values with defaults and track user-provided status
-        DescribeEntities = describeEntities ?? DEFAULT_ENABLED;
+        // Track user-provided status - only true if the parameter was not null
         UserProvidedDescribeEntities = describeEntities is not null;
-
-        CreateRecord = createRecord ?? DEFAULT_ENABLED;
         UserProvidedCreateRecord = createRecord is not null;
-
-        ReadRecords = readRecords ?? DEFAULT_ENABLED;
         UserProvidedReadRecords = readRecords is not null;
-
-        UpdateRecord = updateRecord ?? DEFAULT_ENABLED;
         UserProvidedUpdateRecord = updateRecord is not null;
-
-        DeleteRecord = deleteRecord ?? DEFAULT_ENABLED;
         UserProvidedDeleteRecord = deleteRecord is not null;
-
-        ExecuteEntity = executeEntity ?? DEFAULT_ENABLED;
         UserProvidedExecuteEntity = executeEntity is not null;
     }
 
     /// <summary>
     /// Creates a DmlToolsConfig with all tools set to the same state
+    /// Used when user explicitly sets "dml-tools": true/false
     /// </summary>
     public static DmlToolsConfig FromBoolean(bool enabled)
     {
+        // Only pass allToolsEnabled, leave individual tools as null
         return new DmlToolsConfig(
             allToolsEnabled: enabled,
-            describeEntities: enabled,
-            createRecord: enabled,
-            readRecords: enabled,
-            updateRecord: enabled,
-            deleteRecord: enabled,
-            executeEntity: enabled
+            describeEntities: null,
+            createRecord: null,
+            readRecords: null,
+            updateRecord: null,
+            deleteRecord: null,
+            executeEntity: null
         );
     }
 
     /// <summary>
     /// Creates a default DmlToolsConfig with all tools enabled
+    /// Used when dml-tools is not specified in config at all
     /// </summary>
-    public static DmlToolsConfig Default => FromBoolean(DEFAULT_ENABLED);
+    public static DmlToolsConfig Default => new(
+        allToolsEnabled: null,
+        describeEntities: null,
+        createRecord: null,
+        readRecords: null,
+        updateRecord: null,
+        deleteRecord: null,
+        executeEntity: null
+    );
 
     /// <summary>
     /// Flag which informs CLI and JSON serializer whether to write all-tools-enabled
     /// property/value to the runtime config file.
     /// </summary>
     [JsonIgnore(Condition = JsonIgnoreCondition.Always)]
     [MemberNotNullWhen(true, nameof(AllToolsEnabled))]
-    public bool UserProvidedAllToolsEnabled { get; init; } = false;
+    public bool UserProvidedAllTools { get; init; } = false;
 
     /// <summary>
     /// Flag which informs CLI and JSON serializer whether to write describe-entities

src/Config/ObjectModel/McpRuntimeOptions.cs

@@ -32,11 +32,11 @@ public record McpRuntimeOptions
 
     [JsonConstructor]
     public McpRuntimeOptions(
-        bool Enabled = true,
+        bool? Enabled = null,
         string? Path = null,
         DmlToolsConfig? DmlTools = null)
     {
-        this.Enabled = Enabled;
+        this.Enabled = Enabled ?? true;
 
         if (Path is not null)
         {
@@ -51,7 +51,8 @@ public McpRuntimeOptions(
         // if DmlTools is null, set All tools enabled by default
         if (DmlTools is null)
         {
-            this.DmlTools = DmlToolsConfig.FromBoolean(DmlToolsConfig.DEFAULT_ENABLED);
+            // Use Default instead of FromBoolean to avoid setting UserProvided flags
+            this.DmlTools = DmlToolsConfig.Default;
         }
         else
         {