Refactor setup and tool helpers for improved modularity and clarity

- Moved setup logic into dedicated files: agent.ts, config.ts, index.ts, workspace.ts.
- Introduced tool-helpers.ts for shared functions across tools, reducing boilerplate.
- Updated tools (status, task-comment, task-create, task-update, work-finish, work-start) to utilize new helper functions for workspace resolution and provider creation.
- Enhanced error handling and context detection in tools.
- Improved project resolution logic to streamline tool execution.
- Added new functionality for agent creation and configuration management in setup.

lib/tiers.ts

@@ -46,7 +46,7 @@ export function isDevTier(value: string): value is DevTier {
  * 2. DEFAULT_MODELS (hardcoded defaults)
  * 3. Treat input as raw model ID (passthrough for non-tier values)
  */
-export function resolveModel(
+export function resolveTierToModel(
   tier: string,
   pluginConfig?: Record<string, unknown>,
 ): string {