Audit core.warning/core.error usage (#269)

* Stop using command-based logs for warnings and errors

Co-authored-by: Cursor <cursoragent@cursor.com>

* revert

* tweak

* de-noise

* Remove redundant ts() timestamp prefix from log calls

* Restore timestamped logging and refine debug output routing.

Bring back timestamp prefixes for standard logs and make log.debug emit via core.debug when runner debug is enabled, while still surfacing debug lines for --debug runs.

Co-authored-by: Cursor <cursoragent@cursor.com>

---------

Co-authored-by: Mateusz Burzyński <mateuszburzynski@gmail.com>
Co-authored-by: Cursor <cursoragent@cursor.com>
Co-authored-by: pullfrog[bot] <226033991+pullfrog[bot]@users.noreply.github.com>
Co-authored-by: Colin McDonnell <colinmcd94@gmail.com>

mcp/reviewComments.ts

@@ -632,7 +632,7 @@ export function ResolveReviewThreadTool(ctx: ToolContext) {
         const message = isResolved
           ? `thread ${params.thread_id} was already resolved`
           : `failed to resolve thread ${params.thread_id}: ${errorMessage}`;
-        log.warning(message);
+        log.info(message);
 
         return {
           thread_id: params.thread_id,