Agents: move bootstrap warnings out of system prompt (#48753)

Merged via squash.

Prepared head SHA: dc1d4d075a
Co-authored-by: scoootscooob <167050519+scoootscooob@users.noreply.github.com>
Reviewed-by: @scoootscooob

src/agents/cli-runner.ts

@@ -15,6 +15,7 @@ import {
   buildBootstrapInjectionStats,
   buildBootstrapPromptWarning,
   buildBootstrapTruncationReportMeta,
+  prependBootstrapPromptWarning,
 } from "./bootstrap-budget.js";
 import { makeBootstrapWarn, resolveBootstrapContextForRun } from "./bootstrap-files.js";
 import { resolveCliBackendConfig } from "./cli-backends.js";
@@ -162,7 +163,6 @@ export async function runCliAgent(params: {
     docsPath: docsPath ?? undefined,
     tools: [],
     contextFiles,
-    bootstrapTruncationWarningLines: bootstrapPromptWarning.lines,
     modelDisplay,
     agentId: sessionAgentId,
   });
@@ -218,7 +218,9 @@ export async function runCliAgent(params: {
 
     let imagePaths: string[] | undefined;
     let cleanupImages: (() => Promise<void>) | undefined;
-    let prompt = params.prompt;
+    let prompt = prependBootstrapPromptWarning(params.prompt, bootstrapPromptWarning.lines, {
+      preserveExactPrompt: heartbeatPrompt,
+    });
     if (params.images && params.images.length > 0) {
       const imagePayload = await writeCliImages(params.images);
       imagePaths = imagePayload.paths;