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.buildbootstrapcontextfiles.e2e.test.ts

@@ -14,7 +14,7 @@ describe("buildBootstrapContextFiles", () => {
     const files = [makeFile({ missing: true, content: undefined })];
     expect(buildBootstrapContextFiles(files)).toEqual([
       {
-        path: DEFAULT_AGENTS_FILENAME,
+        path: "/tmp/AGENTS.md",
         content: "[MISSING] Expected at: /tmp/AGENTS.md",
       },
     ]);