@@ -405,7 +405,7 @@ func TestGetEngineOption_AllBuiltInEngines(t *testing.T) {
 		{string(CopilotEngine), "GitHub Copilot", CopilotGitHubToken, nil},
 		{string(ClaudeEngine), "Claude", AnthropicAPIKey, []string{}},
 		{string(CodexEngine), "Codex", OpenAIAPIKey, []string{CodexAPIKey}},
-		{string(GeminiEngine), "Gemini", GeminiAPIKey, nil},
+		{string(GeminiEngine), "Gemini (Deprecated)", GeminiAPIKey, nil},
 		{string(PiEngine), "Pi", CopilotGitHubToken, []string{AnthropicAPIKey, OpenAIAPIKey, CodexAPIKey, GeminiAPIKey}},
 	}
 
 
@@ -85,9 +85,7 @@ func (c *Compiler) setupEngineAndImports(result *parser.FrontmatterResult, clean
 	if err := c.runPostEngineValidations(result.Frontmatter, engineSetting, engineConfig, networkPermissions, sandboxConfig, agenticEngine, importsResult); err != nil {
 		return nil, err
 	}
-	if agenticEngine.GetID() == string(constants.GeminiEngine) {
-		fmt.Fprintln(os.Stderr, console.FormatInfoMessage("The gemini engine is deprecated in favor of the experimental agy engine. Use engine: agy where supported; retain engine: gemini for Google WIF or features Agy does not support. See https://github.github.com/gh-aw/engines/agy/"))
-	}
+	c.emitGeminiDeprecationNotice(agenticEngine)
 	return &engineSetupResult{
 		engineSetting:      engineSetting,
 		model:              model,
@@ -100,6 +98,17 @@ func (c *Compiler) setupEngineAndImports(result *parser.FrontmatterResult, clean
 	}, nil
 }
 
+func (c *Compiler) emitGeminiDeprecationNotice(engine CodingAgentEngine) {
+	if engine.GetID() != string(constants.GeminiEngine) {
+		return
+	}
+	if c.batchMode {
+		c.featureUsage["gemini deprecation"]++
+	} else if !c.quiet {
+		fmt.Fprintln(os.Stderr, console.FormatInfoMessageStderr("The gemini engine is deprecated in favor of the experimental agy engine. Use engine: agy where supported; retain engine: gemini for Google WIF or features Agy does not support. See https://github.github.com/gh-aw/engines/agy/"))
+	}
+}
+
 // Import defaults can still change the engine config after this typo check.
 // Imported definitions are registered later and must skip early resolution.
 func (c *Compiler) validateEarlyEngineSetting(frontmatter map[string]any, engineSetting string, engineConfig *EngineConfig) error {
 
@@ -21,15 +21,20 @@ func TestSetupEngineAndImports_GeminiDeprecation(t *testing.T) {
 		engine       string
 		imported     bool
 		override     string
+		batchMode    bool
+		quiet        bool
 		wantEngine   string
 		wantNotices  int
+		wantBatchUse int
 		wantWarnings int
 	}{
 		{name: "string form", engine: "engine: gemini\n", wantEngine: "gemini", wantNotices: 1},
 		{name: "object form with pin", engine: "engine:\n  id: gemini\n  version: \"0.39.1\"\n", wantEngine: "gemini", wantNotices: 1},
 		{name: "imported engine", imported: true, wantEngine: "gemini", wantNotices: 1},
 		{name: "override to Gemini", engine: "engine: copilot\n", override: "gemini", wantEngine: "gemini", wantNotices: 1, wantWarnings: 1},
 		{name: "override away from Gemini", engine: "engine: gemini\n", override: "copilot", wantEngine: "copilot", wantWarnings: 1},
+		{name: "batch mode aggregates notice", engine: "engine: gemini\n", batchMode: true, wantEngine: "gemini", wantBatchUse: 1},
+		{name: "quiet mode suppresses notice", engine: "engine: gemini\n", quiet: true, wantEngine: "gemini"},
 		{name: "default engine", wantEngine: "copilot"},
 		{name: "experimental replacement", engine: "engine: agy\n", wantEngine: "agy"},
 		{
@@ -60,6 +65,8 @@ func TestSetupEngineAndImports_GeminiDeprecation(t *testing.T) {
 			require.NoError(t, err)
 			compiler := NewCompiler(WithEngineOverride(tt.override))
 			compiler.SetStrictMode(true)
+			compiler.SetBatchMode(tt.batchMode)
+			compiler.SetQuiet(tt.quiet)
 			output := testutil.CaptureStderr(t, func() {
 				result, err := compiler.setupEngineAndImports(frontmatter, filepath.Join(tmpDir, "test.md"), []byte(content), tmpDir)
 				require.NoError(t, err)
@@ -76,6 +83,7 @@ func TestSetupEngineAndImports_GeminiDeprecation(t *testing.T) {
 				}
 			})
 			assert.Equal(t, tt.wantNotices, strings.Count(output, "The gemini engine is deprecated"))
+			assert.Equal(t, tt.wantBatchUse, compiler.GetExperimentalFeatureUsage()["gemini deprecation"])
 			assert.Equal(t, tt.wantWarnings, compiler.GetWarningCount())
 			if tt.wantNotices > 0 {
 				assert.Contains(t, output, "Use engine: agy where supported")
Original file line number	Diff line number	Diff line change
`@@ -405,7 +405,7 @@ func TestGetEngineOption_AllBuiltInEngines(t *testing.T) {`
`405`	`405`	`{string(CopilotEngine), "GitHub Copilot", CopilotGitHubToken, nil},`
`406`	`406`	`{string(ClaudeEngine), "Claude", AnthropicAPIKey, []string{}},`
`407`	`407`	`{string(CodexEngine), "Codex", OpenAIAPIKey, []string{CodexAPIKey}},`
`408`		`- {string(GeminiEngine), "Gemini", GeminiAPIKey, nil},`
	`408`	`+ {string(GeminiEngine), "Gemini (Deprecated)", GeminiAPIKey, nil},`
`409`	`409`	`{string(PiEngine), "Pi", CopilotGitHubToken, []string{AnthropicAPIKey, OpenAIAPIKey, CodexAPIKey, GeminiAPIKey}},`
`410`	`410`	`}`
`411`	`411`