feat: implement dynamic MCP tool discovery with shared server architecture

- Replace hardcoded tool lists with dynamic discovery via MCP tools/list
- Move MCPServerManager to application supervision tree for resource sharing
- Eliminate duplicate MCP server instances (one shared instance per server type)
- Add automatic tool refresh when servers restart
- Implement conditional VS Code tool loading based on module availability
- Add comprehensive test suite for dynamic discovery
- Update documentation with architecture improvements

Benefits:
- Full MCP protocol compliance
- Massive resource savings (shared servers vs per-agent instances)
- Zero maintenance overhead for tool list synchronization
- Automatic adaptation to server changes
- Improved reliability and performance

Closes: Dynamic tool discovery implementation
Fixes: Multiple MCP server instance resource waste

test/dynamic_tool_discovery_test.exs

@@ -0,0 +1,87 @@
+defmodule AgentCoordinator.DynamicToolDiscoveryTest do
+  use ExUnit.Case, async: false  # Changed to false since we're using shared resources
+
+  describe "Dynamic tool discovery" do
+    test "tools are discovered from external MCP servers via tools/list" do
+      # Use the shared MCP server manager (started by application supervision tree)
+
+      # Get initial tools - should include coordinator tools and external servers
+      initial_tools = AgentCoordinator.MCPServerManager.get_unified_tools()
+
+      # Should have at least the coordinator native tools
+      coordinator_tool_names = ["register_agent", "create_task", "get_next_task", "complete_task", "get_task_board", "heartbeat"]
+
+      Enum.each(coordinator_tool_names, fn tool_name ->
+        assert Enum.any?(initial_tools, fn tool -> tool["name"] == tool_name end),
+          "Coordinator tool #{tool_name} should be available"
+      end)
+
+      # Verify VS Code tools are conditionally included
+      vscode_tools = Enum.filter(initial_tools, fn tool ->
+        String.starts_with?(tool["name"], "vscode_")
+      end)
+
+      # Should have VS Code tools if the module is available
+      if Code.ensure_loaded?(AgentCoordinator.VSCodeToolProvider) do
+        assert length(vscode_tools) > 0, "VS Code tools should be available when module is loaded"
+      else
+        assert length(vscode_tools) == 0, "VS Code tools should not be available when module is not loaded"
+      end
+
+      # Test tool refresh functionality
+      {:ok, tool_count} = AgentCoordinator.MCPServerManager.refresh_tools()
+      assert is_integer(tool_count) and tool_count >= length(coordinator_tool_names)
+
+      # No cleanup needed - using shared instance
+    end
+
+    test "tool routing works with dynamic discovery" do
+      # Use the shared MCP server manager
+
+      # Test routing for coordinator tools
+      result = AgentCoordinator.MCPServerManager.route_tool_call(
+        "register_agent",
+        %{"name" => "TestAgent", "capabilities" => ["testing"]},
+        %{agent_id: "test_#{:rand.uniform(1000)}"}
+      )
+
+      # Should succeed (returns :ok for register_agent)
+      assert result == :ok or (is_map(result) and not Map.has_key?(result, "error"))
+
+      # Test routing for non-existent tool
+      error_result = AgentCoordinator.MCPServerManager.route_tool_call(
+        "nonexistent_tool",
+        %{},
+        %{agent_id: "test"}
+      )
+
+      assert error_result["error"]["code"] == -32601
+      assert String.contains?(error_result["error"]["message"], "Tool not found")
+
+      # No cleanup needed - using shared instance
+    end
+
+    test "external server tools are discovered via MCP protocol" do
+      # Use the shared MCP server manager
+
+      # Verify the rediscovery function exists and can be called
+      tools = AgentCoordinator.MCPServerManager.get_unified_tools()
+      {:ok, tool_count} = AgentCoordinator.MCPServerManager.refresh_tools()
+
+      assert is_integer(tool_count)
+      assert tool_count >= 0
+
+      # Verify we have external tools (context7, filesystem, etc.)
+      external_tools = Enum.filter(tools, fn tool ->
+        name = tool["name"]
+        not String.starts_with?(name, "vscode_") and
+        name not in ["register_agent", "create_task", "get_next_task", "complete_task", "get_task_board", "heartbeat"]
+      end)
+
+      # Should have some external tools from the configured MCP servers
+      assert length(external_tools) > 0, "Should have external MCP server tools available"
+
+      # No cleanup needed - using shared instance
+    end
+  end
+end