diff --git a/src/config/schema.ts b/src/config/schema.ts
index 5a2010b..b6fd60b 100644
--- a/src/config/schema.ts
+++ b/src/config/schema.ts
@@ -115,6 +115,11 @@ export const SisyphusAgentConfigSchema = z.object({
   replace_plan: z.boolean().optional(),
 })
 
+export const CommentCheckerConfigSchema = z.object({
+  /** Custom prompt to replace the default warning message. Use {{comments}} placeholder for detected comments XML. */
+  custom_prompt: z.string().optional(),
+})
+
 export const DynamicContextPruningConfigSchema = z.object({
   /** Enable dynamic context pruning (default: false) */
   enabled: z.boolean().default(false),
@@ -175,6 +180,7 @@ export const OhMyOpenCodeConfigSchema = z.object({
   claude_code: ClaudeCodeConfigSchema.optional(),
   google_auth: z.boolean().optional(),
   sisyphus_agent: SisyphusAgentConfigSchema.optional(),
+  comment_checker: CommentCheckerConfigSchema.optional(),
   experimental: ExperimentalConfigSchema.optional(),
   auto_update: z.boolean().optional(),
 })
@@ -185,6 +191,7 @@ export type AgentOverrides = z.infer<typeof AgentOverridesSchema>
 export type AgentName = z.infer<typeof AgentNameSchema>
 export type HookName = z.infer<typeof HookNameSchema>
 export type SisyphusAgentConfig = z.infer<typeof SisyphusAgentConfigSchema>
+export type CommentCheckerConfig = z.infer<typeof CommentCheckerConfigSchema>
 export type ExperimentalConfig = z.infer<typeof ExperimentalConfigSchema>
 export type DynamicContextPruningConfig = z.infer<typeof DynamicContextPruningConfigSchema>
 
diff --git a/src/hooks/comment-checker/index.ts b/src/hooks/comment-checker/index.ts
index 033d4b9..834f685 100644
--- a/src/hooks/comment-checker/index.ts
+++ b/src/hooks/comment-checker/index.ts
@@ -1,5 +1,6 @@
 import type { PendingCall } from "./types"
 import { runCommentChecker, getCommentCheckerPath, startBackgroundInit, type HookInput } from "./cli"
+import type { CommentCheckerConfig } from "../../config/schema"
 
 import * as fs from "fs"
 import { existsSync } from "fs"
@@ -32,8 +33,8 @@ function cleanupOldPendingCalls(): void {
 
 setInterval(cleanupOldPendingCalls, 10_000)
 
-export function createCommentCheckerHooks() {
-  debugLog("createCommentCheckerHooks called")
+export function createCommentCheckerHooks(config?: CommentCheckerConfig) {
+  debugLog("createCommentCheckerHooks called", { config })
   
   // Start background CLI initialization (may trigger lazy download)
   startBackgroundInit()
@@ -123,7 +124,7 @@ export function createCommentCheckerHooks() {
         
         // CLI mode only
         debugLog("using CLI:", cliPath)
-        await processWithCli(input, pendingCall, output, cliPath)
+        await processWithCli(input, pendingCall, output, cliPath, config?.custom_prompt)
       } catch (err) {
         debugLog("tool.execute.after failed:", err)
       }
@@ -135,7 +136,8 @@ async function processWithCli(
   input: { tool: string; sessionID: string; callID: string },
   pendingCall: PendingCall,
   output: { output: string },
-  cliPath: string
+  cliPath: string,
+  customPrompt?: string
 ): Promise<void> {
   debugLog("using CLI mode with path:", cliPath)
   
@@ -154,7 +156,7 @@ async function processWithCli(
     },
   }
   
-  const result = await runCommentChecker(hookInput, cliPath)
+  const result = await runCommentChecker(hookInput, cliPath, customPrompt)
   
   if (result.hasComments && result.message) {
     debugLog("CLI detected comments, appending message")
diff --git a/src/hooks/thinking-block-validator/index.ts b/src/hooks/thinking-block-validator/index.ts
index 463d3a8..8e92738 100644
--- a/src/hooks/thinking-block-validator/index.ts
+++ b/src/hooks/thinking-block-validator/index.ts
@@ -51,14 +51,15 @@ function isExtendedThinkingModel(modelID: string): boolean {
 }
 
 /**
- * Check if a message has tool parts (tool_use)
+ * Check if a message has any content parts (tool_use, text, or other non-thinking content)
  */
-function hasToolParts(parts: Part[]): boolean {
+function hasContentParts(parts: Part[]): boolean {
   if (!parts || parts.length === 0) return false
 
   return parts.some((part: Part) => {
     const type = part.type as string
-    return type === "tool" || type === "tool_use"
+    // Include tool parts and text parts (anything that's not thinking/reasoning)
+    return type === "tool" || type === "tool_use" || type === "text"
   })
 }
 
@@ -154,8 +155,8 @@ export function createThinkingBlockValidatorHook(): MessagesTransformHook {
         // Only check assistant messages
         if (msg.info.role !== "assistant") continue
 
-        // Check if message has tool parts but doesn't start with thinking
-        if (hasToolParts(msg.parts) && !startsWithThinkingBlock(msg.parts)) {
+        // Check if message has content parts but doesn't start with thinking
+        if (hasContentParts(msg.parts) && !startsWithThinkingBlock(msg.parts)) {
           // Find thinking content from previous turns
           const previousThinking = findPreviousThinkingContent(messages, i)