fix: deprecate --*.disabled CLI flags, wire up --mcp.disabled (#3482)

## Why make this change?

- Closes #3376

`dab init` has both `--rest.disabled` and `--rest.enabled` (same for
graphql/mcp) for the same property. This is confusing UX. Additionally,
`--mcp.disabled` was defined but never wired up (no-op).

## What is this change?

- **Hide** `--rest.disabled`, `--graphql.disabled`, `--mcp.disabled`
from `--help` output (`Hidden = true`)
- **Add `[Deprecated]` prefix** to HelpText for all three flags
- **Add deprecation warning** for `--mcp.disabled` (was missing — REST
and GraphQL already had them)
- **Wire up `--mcp.disabled`** through `TryDetermineIfApiIsEnabled` (was
previously a no-op)
- **Remove** unused `TryDetermineIfMcpIsEnabled` helper
- **Fix** REST+GraphQL disabled-together check to use resolved `enabled`
booleans instead of raw `Disabled` flags

### Breaking change analysis
- **Non-breaking**: All `--*.disabled` flags still work — they are just
hidden from `--help`
- **Behavior fix for MCP**: `--mcp.disabled` was previously a no-op; now
it actually disables MCP
- **Existing scripts**: Will continue working; deprecation warnings
appear in logs

## How was this tested?

- [x] Unit tests
- [ ] Integration tests

## Sample Request(s)

NA

Author: souvikghosh04

src/Cli.Tests/EndToEndTests.cs

@@ -1288,6 +1288,11 @@ public void TestBaseRouteIsConfigurableForSWA(string authProvider, bool isExcept
     [DataRow(ApiType.GraphQL, true, false, true, false, DisplayName = "Validate that GraphQL endpoint is disabled when enabled option is omitted and disabled option is included in the init command.")]
     [DataRow(ApiType.GraphQL, true, true, false, false, DisplayName = "Validate that GraphQL endpoint is disabled when enabled option is set to false and disabled option is included in the init command.")]
     [DataRow(ApiType.GraphQL, true, true, true, true, true, DisplayName = "Validate that config generation fails when enabled and disabled options provide conflicting values for GraphQL endpoint.")]
+    [DataRow(ApiType.MCP, false, false, true, true, DisplayName = "Validate that MCP endpoint is enabled when both enabled and disabled options are omitted from the init command.")]
+    [DataRow(ApiType.MCP, false, true, true, true, DisplayName = "Validate that MCP endpoint is enabled when enabled option is set to true and disabled option is omitted from the init command.")]
+    [DataRow(ApiType.MCP, true, false, true, false, DisplayName = "Validate that MCP endpoint is disabled when enabled option is omitted and disabled option is included in the init command.")]
+    [DataRow(ApiType.MCP, true, true, false, false, DisplayName = "Validate that MCP endpoint is disabled when enabled option is set to false and disabled option is included in the init command.")]
+    [DataRow(ApiType.MCP, true, true, true, true, true, DisplayName = "Validate that config generation fails when enabled and disabled options provide conflicting values for MCP endpoint.")]
     public void TestEnabledDisabledFlagsForApis(
         ApiType apiType,
         bool includeDisabledFlag,
@@ -1333,12 +1338,22 @@ public void TestEnabledDisabledFlagsForApis(
                 Assert.IsNotNull(runtimeConfig.Runtime.Rest);
                 Assert.AreEqual(expectedEnabledFlagValueInConfig, runtimeConfig.Runtime.Rest.Enabled);
             }
-            else
+            else if (apiType is ApiType.GraphQL)
             {
                 Assert.IsNotNull(runtimeConfig.Runtime);
                 Assert.IsNotNull(runtimeConfig.Runtime.GraphQL);
                 Assert.AreEqual(expectedEnabledFlagValueInConfig, runtimeConfig.Runtime.GraphQL.Enabled);
             }
+            else if (apiType is ApiType.MCP)
+            {
+                Assert.IsNotNull(runtimeConfig.Runtime);
+                Assert.IsNotNull(runtimeConfig.Runtime.Mcp);
+                Assert.AreEqual(expectedEnabledFlagValueInConfig, runtimeConfig.Runtime.Mcp.Enabled);
+            }
+            else
+            {
+                Assert.Fail($"Unexpected ApiType value '{apiType}' in test.");
+            }
         }
     }
 

src/Cli.Tests/InitTests.cs

@@ -196,20 +196,24 @@ public void VerifyRequiredOptionsForCosmosDbNoSqlDatabase(
         }
 
         /// <summary>
-        /// Verify that if both REST and GraphQL is disabled, we will get error.
+        /// Verify that if all APIs (REST, GraphQL, and MCP) are disabled, we will get an error.
+        /// Disabling only REST and GraphQL is allowed when MCP remains enabled.
         /// </summary>
-        [DataRow(CliBool.False, CliBool.False, false, DisplayName = "Both REST and GraphQL disabled.")]
-        [DataRow(CliBool.False, CliBool.True, true, DisplayName = "REST disabled, and GraphQL enabled.")]
-        [DataRow(CliBool.True, CliBool.False, true, DisplayName = "REST enabled, and GraphQL disabled.")]
-        [DataRow(CliBool.True, CliBool.True, true, DisplayName = "Both REST and GraphQL are enabled.")]
+        [DataRow(CliBool.False, CliBool.False, CliBool.False, false, DisplayName = "All three APIs disabled - failure.")]
+        [DataRow(CliBool.False, CliBool.False, CliBool.None, true, DisplayName = "REST and GraphQL disabled, MCP defaulted to enabled - success.")]
+        [DataRow(CliBool.False, CliBool.True, CliBool.None, true, DisplayName = "REST disabled, and GraphQL enabled.")]
+        [DataRow(CliBool.True, CliBool.False, CliBool.None, true, DisplayName = "REST enabled, and GraphQL disabled.")]
+        [DataRow(CliBool.True, CliBool.True, CliBool.None, true, DisplayName = "Both REST and GraphQL are enabled.")]
         [DataTestMethod]
-        public void EnsureFailureWhenBothRestAndGraphQLAreDisabled(
+        public void EnsureFailureWhenAllApisAreDisabled(
             CliBool restEnabled,
             CliBool graphQLEnabled,
+            CliBool mcpEnabled,
             bool expectedResult)
         {
             bool restDisabled = restEnabled is CliBool.False ? true : false;
             bool graphQLDisabled = graphQLEnabled is CliBool.False ? true : false;
+            bool mcpDisabled = mcpEnabled is CliBool.False ? true : false;
             InitOptions options = new(
                 databaseType: DatabaseType.MSSQL,
                 connectionString: "testconnectionstring",
@@ -222,8 +226,10 @@ public void EnsureFailureWhenBothRestAndGraphQLAreDisabled(
                 authenticationProvider: EasyAuthType.AppService.ToString(),
                 restEnabled: restEnabled,
                 graphqlEnabled: graphQLEnabled,
+                mcpEnabled: mcpEnabled,
                 restDisabled: restDisabled,
                 graphqlDisabled: graphQLDisabled,
+                mcpDisabled: mcpDisabled,
                 config: TEST_RUNTIME_CONFIG_FILE);
 
             Assert.AreEqual(expectedResult, TryCreateRuntimeConfig(options, _runtimeConfigLoader!, _fileSystem!, out RuntimeConfig? _));

src/Cli/Commands/InitOptions.cs

@@ -111,19 +111,19 @@ public InitOptions(
         [Option("runtime.base-route", Default = null, Required = false, HelpText = "Specifies the base route for API requests.")]
         public string? RuntimeBaseRoute { get; }
 
-        [Option("rest.disabled", Default = false, Required = false, HelpText = "Disables REST endpoint for all entities.")]
+        [Option("rest.disabled", Default = false, Required = false, Hidden = true, HelpText = "[Deprecated] Use --rest.enabled false instead. Disables REST endpoint for all entities.")]
         public bool RestDisabled { get; }
 
         [Option("graphql.path", Default = GraphQLRuntimeOptions.DEFAULT_PATH, Required = false, HelpText = "Specify the GraphQL endpoint's default prefix.")]
         public string GraphQLPath { get; }
 
-        [Option("graphql.disabled", Default = false, Required = false, HelpText = "Disables GraphQL endpoint for all entities.")]
+        [Option("graphql.disabled", Default = false, Required = false, Hidden = true, HelpText = "[Deprecated] Use --graphql.enabled false instead. Disables GraphQL endpoint for all entities.")]
         public bool GraphQLDisabled { get; }
 
         [Option("mcp.path", Default = McpRuntimeOptions.DEFAULT_PATH, Required = false, HelpText = "Specify the MCP endpoint's default prefix.")]
         public string McpPath { get; }
 
-        [Option("mcp.disabled", Default = false, Required = false, HelpText = "Disables MCP endpoint for all entities.")]
+        [Option("mcp.disabled", Default = false, Required = false, Hidden = true, HelpText = "[Deprecated] Use --mcp.enabled false instead. Disables MCP endpoint for all entities.")]
         public bool McpDisabled { get; }
 
         [Option("rest.enabled", Required = false, HelpText = "(Default: true) Enables REST endpoint for all entities. Supported values: true, false.")]

src/Cli/ConfigGenerator.cs

@@ -100,24 +100,31 @@ public static bool TryCreateRuntimeConfig(InitOptions options, FileSystemRuntime
 
             HyphenatedNamingPolicy namingPolicy = new();
 
-            // If --rest.disabled flag is included in the init command, we log a warning to not use this flag as it will be deprecated in future versions of DAB.
+            // If --rest.disabled flag is included in the init command, we log a warning as the flag is deprecated.
             if (options.RestDisabled is true)
             {
-                _logger.LogWarning("The option --rest.disabled will be deprecated and support for the option will be removed in future versions of Data API builder." +
-                    " We recommend that you use the --rest.enabled option instead.");
+                _logger.LogWarning("The option --rest.disabled is deprecated and support for the option will be removed in future versions of Data API builder." +
+                    " Use the --rest.enabled option instead.");
             }
 
-            // If --graphql.disabled flag is included in the init command, we log a warning to not use this flag as it will be deprecated in future versions of DAB.
+            // If --graphql.disabled flag is included in the init command, we log a warning as the flag is deprecated.
             if (options.GraphQLDisabled is true)
             {
-                _logger.LogWarning("The option --graphql.disabled will be deprecated and support for the option will be removed in future versions of Data API builder." +
-                    " We recommend that you use the --graphql.enabled option instead.");
+                _logger.LogWarning("The option --graphql.disabled is deprecated and support for the option will be removed in future versions of Data API builder." +
+                    " Use the --graphql.enabled option instead.");
+            }
+
+            // If --mcp.disabled flag is included in the init command, we log a warning as the flag is deprecated.
+            if (options.McpDisabled is true)
+            {
+                _logger.LogWarning("The option --mcp.disabled is deprecated and support for the option will be removed in future versions of Data API builder." +
+                    " Use the --mcp.enabled option instead.");
             }
 
             bool restEnabled, graphQLEnabled, mcpEnabled;
             if (!TryDetermineIfApiIsEnabled(options.RestDisabled, options.RestEnabled, ApiType.REST, out restEnabled) ||
                 !TryDetermineIfApiIsEnabled(options.GraphQLDisabled, options.GraphQLEnabled, ApiType.GraphQL, out graphQLEnabled) ||
-                !TryDetermineIfMcpIsEnabled(options.McpEnabled, out mcpEnabled))
+                !TryDetermineIfApiIsEnabled(options.McpDisabled, options.McpEnabled, ApiType.MCP, out mcpEnabled))
             {
                 return false;
             }
@@ -237,9 +244,9 @@ public static bool TryCreateRuntimeConfig(InitOptions options, FileSystemRuntime
                 }
             }
 
-            if (options.RestDisabled && options.GraphQLDisabled)
+            if (!restEnabled && !graphQLEnabled && !mcpEnabled)
             {
-                _logger.LogError("Both Rest and GraphQL cannot be disabled together.");
+                _logger.LogError("At least one of REST, GraphQL, or MCP must be enabled.");
                 return false;
             }
 
@@ -297,12 +304,12 @@ public static bool TryCreateRuntimeConfig(InitOptions options, FileSystemRuntime
 
         /// <summary>
         /// Helper method to determine if the api is enabled or not based on the enabled/disabled options in the dab init command.
-        /// The method also validates that there is no mismatch in semantics of enabling/disabling the REST/GraphQL API(s)
+        /// The method also validates that there is no mismatch in semantics of enabling/disabling the REST/GraphQL/MCP API(s)
         /// based on the values supplied in the enabled/disabled options for the API in the init command.
         /// </summary>
         /// <param name="apiDisabledOptionValue">Value of disabled option as in the init command. If the option is omitted in the command, default value is assigned.</param>
         /// <param name="apiEnabledOptionValue">Value of enabled option as in the init command. If the option is omitted in the command, default value is assigned.</param>
-        /// <param name="apiType">ApiType - REST/GraphQL.</param>
+        /// <param name="apiType">ApiType - REST/GraphQL/MCP.</param>
         /// <param name="isApiEnabled">Boolean value indicating whether the API endpoint is enabled or not.</param>
         private static bool TryDetermineIfApiIsEnabled(bool apiDisabledOptionValue, CliBool apiEnabledOptionValue, ApiType apiType, out bool isApiEnabled)
         {
@@ -334,17 +341,6 @@ private static bool TryDetermineIfApiIsEnabled(bool apiDisabledOptionValue, CliB
             return true;
         }
 
-        /// <summary>
-        /// Helper method to determine if the mcp api is enabled or not based on the enabled/disabled options in the dab init command.
-        /// </summary>
-        /// <param name="mcpEnabledOptionValue">True, if MCP is enabled</param>
-        /// <param name="isMcpEnabled">Out param isMcpEnabled</param>
-        /// <returns>True if MCP is enabled</returns>
-        private static bool TryDetermineIfMcpIsEnabled(CliBool mcpEnabledOptionValue, out bool isMcpEnabled)
-        {
-            return TryDetermineIfApiIsEnabled(false, mcpEnabledOptionValue, ApiType.MCP, out isMcpEnabled);
-        }
-
         /// <summary>
         /// Helper method to determine if the multiple create operation is enabled or not based on the inputs from dab init command.
         /// </summary>