[MCP] Prevent duplicating entities between custom tools and describe_entities

src/Azure.DataApiBuilder.Mcp/BuiltInTools/DescribeEntitiesTool.cs

@@ -146,6 +146,10 @@ public Task<CallToolResult> ExecuteAsync(
 
                 List<Dictionary<string, object?>> entityList = new();
 
+                // Track how many stored procedures were filtered out because they're exposed as custom-tool-only.
+                // This helps provide a more specific error message when all entities are filtered.
+                int filteredCustomToolCount = 0;
+
                 if (runtimeConfig.Entities != null)
                 {
                     foreach (KeyValuePair<string, Entity> entityEntry in runtimeConfig.Entities)
@@ -155,6 +159,18 @@ public Task<CallToolResult> ExecuteAsync(
                         string entityName = entityEntry.Key;
                         Entity entity = entityEntry.Value;
 
+                        // Filter out stored procedures when dml-tools is explicitly disabled (false).
+                        // This applies regardless of custom-tool setting:
+                        // - custom-tool: true, dml-tools: false → Filtered (appears only in tools/list)
+                        // - custom-tool: false, dml-tools: false → Filtered (entity fully disabled for MCP)
+                        // When dml-tools is true (or default), the entity appears in describe_entities.
+                        if (entity.Source.Type == EntitySourceType.StoredProcedure &&
+                            entity.Mcp?.DmlToolEnabled == false)
+                        {
+                            filteredCustomToolCount++;
+                            continue;
+                        }
+
                         if (!ShouldIncludeEntity(entityName, entityFilter))
                         {
                             continue;
@@ -177,6 +193,7 @@ public Task<CallToolResult> ExecuteAsync(
 
                 if (entityList.Count == 0)
                 {
+                    // No entities matched the filter criteria
                     if (entityFilter != null && entityFilter.Count > 0)
                     {
                         return Task.FromResult(McpResponseBuilder.BuildErrorResult(
@@ -185,6 +202,20 @@ public Task<CallToolResult> ExecuteAsync(
                             $"No entities found matching the filter: {string.Join(", ", entityFilter)}",
                             logger));
                     }
+                    // All entities were filtered because they're custom-tool-only - only return this specific error
+                    // if ALL configured entities were filtered (not just some). This prevents misleading errors
+                    // when entities fail to build for other reasons (e.g., exceptions in Build*EntityInfo).
+                    else if (filteredCustomToolCount > 0 &&
+                             runtimeConfig.Entities != null &&
+                             filteredCustomToolCount == runtimeConfig.Entities.Entities.Count)
+                    {
+                        return Task.FromResult(McpResponseBuilder.BuildErrorResult(
+                            toolName,
+                            "AllEntitiesFilteredAsCustomTools",
+                            $"All {filteredCustomToolCount} configured entities are stored procedures exposed as custom-tool-only (dml-tools: false). Custom tools appear in tools/list, not describe_entities. Use the tools/list endpoint to discover available custom tools.",
+                            logger));
+                    }
+                    // Truly no entities configured in the runtime config, or entities failed to build for other reasons
                     else
                     {
                         return Task.FromResult(McpResponseBuilder.BuildErrorResult(