Improve readability issues

This is only the first change of many changes.

* Remove redundant autogenerated comments
* Use the recommended file name style
* Use camelCase for variable names
* Don't introduce submodules for relevant types
* Don't introduce constants like modules, these are implementation details
* Remove empty files

packages/cli/src/tools/tool-registry.ts

@@ -1,6 +1,5 @@
 import { ToolListUnion, FunctionDeclaration } from '@google/genai';
-import { Tool } from './Tool.js';
-import { ToolResult } from './ToolResult.js';
+import { Tool } from './tool.js';
 
 class ToolRegistry {
     private tools: Map<string, Tool> = new Map();