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/index.ts

@@ -25,7 +25,7 @@ export {
 	createAgentSessionFromServices,
 	createAgentSessionServices,
 } from "./agent-session-services.js";
-export { type BashExecutorOptions, type BashResult, executeBash, executeBashWithOperations } from "./bash-executor.js";
+export { type BashExecutorOptions, type BashResult, executeBashWithOperations } from "./bash-executor.js";
 export type { CompactionResult } from "./compaction/index.js";
 export { createEventBus, type EventBus, type EventBusController } from "./event-bus.js";
 // Extensions system