fix: preserve bootstrap paths and expose failed mutations (#16131)

Merged via /review-pr -> /prepare-pr -> /merge-pr.

Prepared head SHA: 385dcbd8a9
Co-authored-by: Swader <1430603+Swader@users.noreply.github.com>
Co-authored-by: gumadeiras <5599352+gumadeiras@users.noreply.github.com>
Reviewed-by: @gumadeiras

src/agents/pi-embedded-helpers/bootstrap.ts

@@ -168,7 +168,7 @@ export function buildBootstrapContextFiles(
   for (const file of files) {
     if (file.missing) {
       result.push({
-        path: file.name,
+        path: file.path,
         content: `[MISSING] Expected at: ${file.path}`,
       });
       continue;
@@ -183,7 +183,7 @@ export function buildBootstrapContextFiles(
       );
     }
     result.push({
-      path: file.name,
+      path: file.path,
       content: trimmed.content,
     });
   }