fix(coding-agent): remove process-cwd tool singletons and use tool-name allowlists

- switch SDK/CLI tool selection to name-based allowlists
- apply allowlists across built-in, extension, and SDK tools
- remove ambient process.cwd defaults from core tooling and resource helpers
- update tests, examples, and TUI callers for explicit cwd plumbing
- add regression coverage for extension tool filtering

closes #3452
closes #2835

packages/coding-agent/src/core/tools/read.ts

@@ -271,7 +271,3 @@ export function createReadToolDefinition(
 export function createReadTool(cwd: string, options?: ReadToolOptions): AgentTool<typeof readSchema> {
 	return wrapToolDefinition(createReadToolDefinition(cwd, options));
 }
-
-/** Default read tool using process.cwd() for backwards compatibility. */
-export const readToolDefinition = createReadToolDefinition(process.cwd());
-export const readTool = createReadTool(process.cwd());