diff --git a/packages/ai/src/tools/index.ts b/packages/ai/src/tools/index.ts
index cd910e734..148a77f16 100644
--- a/packages/ai/src/tools/index.ts
+++ b/packages/ai/src/tools/index.ts
@@ -17,3 +17,5 @@ export { lsFiles } from './file-tools/ls-files-tool/ls-files-tool';
 export { grepSearch } from './file-tools/grep-search-tool/grep-search-tool';
 export { bashExecute } from './file-tools';
 export { deleteFiles } from './file-tools/delete-files-tool/delete-files-tool';
+export { checkOffTodoList } from './planning-thinking-tools/check-off-todo-list-tool/check-off-todo-list-tool';
+export { updateClarificationsFile } from './planning-thinking-tools/update-clarifications-file-tool/update-clarifications-file-tool';
diff --git a/packages/ai/src/tools/planning-thinking-tools/check-off-todo-list-tool/check-off-todo-list-tool.test.ts b/packages/ai/src/tools/planning-thinking-tools/check-off-todo-list-tool/check-off-todo-list-tool.test.ts
new file mode 100644
index 000000000..8040cb05d
--- /dev/null
+++ b/packages/ai/src/tools/planning-thinking-tools/check-off-todo-list-tool/check-off-todo-list-tool.test.ts
@@ -0,0 +1,134 @@
+import { RuntimeContext } from '@mastra/core/runtime-context';
+import { beforeEach, describe, expect, it } from 'vitest';
+import type { DocsAgentContext } from '../../../context/docs-agent-context';
+import { checkOffTodoList } from './check-off-todo-list-tool';
+
+describe('checkOffTodoList', () => {
+  let runtimeContext: RuntimeContext<DocsAgentContext>;
+
+  beforeEach(() => {
+    runtimeContext = new RuntimeContext<DocsAgentContext>();
+  });
+
+  it('should check off a todo item successfully', async () => {
+    const initialTodoList = `## Todo List
+- [ ] Write unit tests
+- [ ] Implement feature
+- [ ] Review code`;
+
+    runtimeContext.set('todoList', initialTodoList);
+
+    const result = await checkOffTodoList.execute({
+      context: { todoItem: 'Write unit tests' },
+      runtimeContext,
+    });
+
+    expect(result.success).toBe(true);
+    expect(result.updatedTodoList).toContain('- [x] Write unit tests');
+    expect(result.updatedTodoList).toContain('- [ ] Implement feature');
+    expect(result.updatedTodoList).toContain('- [ ] Review code');
+    expect(result.message).toBe('Successfully checked off: "Write unit tests"');
+
+    // Verify context was updated
+    const updatedContext = runtimeContext.get('todoList');
+    expect(updatedContext).toBe(result.updatedTodoList);
+  });
+
+  it('should return error when todo list is not found in context', async () => {
+    const result = await checkOffTodoList.execute({
+      context: { todoItem: 'Some task' },
+      runtimeContext,
+    });
+
+    expect(result.success).toBe(false);
+    expect(result.updatedTodoList).toBe('');
+    expect(result.message).toBe('No todo list found in context');
+  });
+
+  it('should return error when todo item is not found', async () => {
+    const todoList = `## Todo List
+- [ ] Write unit tests
+- [ ] Implement feature`;
+
+    runtimeContext.set('todoList', todoList);
+
+    const result = await checkOffTodoList.execute({
+      context: { todoItem: 'Non-existent task' },
+      runtimeContext,
+    });
+
+    expect(result.success).toBe(false);
+    expect(result.updatedTodoList).toBe(todoList);
+    expect(result.message).toBe(
+      'Todo item "Non-existent task" not found in the list or already checked off'
+    );
+  });
+
+  it('should not check off an already checked item', async () => {
+    const todoList = `## Todo List
+- [x] Write unit tests
+- [ ] Implement feature`;
+
+    runtimeContext.set('todoList', todoList);
+
+    const result = await checkOffTodoList.execute({
+      context: { todoItem: 'Write unit tests' },
+      runtimeContext,
+    });
+
+    expect(result.success).toBe(false);
+    expect(result.updatedTodoList).toBe(todoList);
+    expect(result.message).toBe(
+      'Todo item "Write unit tests" not found in the list or already checked off'
+    );
+  });
+
+  it('should handle first occurrence when there are duplicates', async () => {
+    const todoList = `## Todo List
+- [ ] Write unit tests for feature A
+- [ ] Write unit tests`;
+
+    runtimeContext.set('todoList', todoList);
+
+    const result = await checkOffTodoList.execute({
+      context: { todoItem: 'Write unit tests for feature A' },
+      runtimeContext,
+    });
+
+    expect(result.success).toBe(true);
+    expect(result.updatedTodoList).toBe(`## Todo List
+- [x] Write unit tests for feature A
+- [ ] Write unit tests`);
+  });
+
+  it('should validate input schema', () => {
+    const validInput = { todoItem: 'Test task' };
+    const parsed = checkOffTodoList.inputSchema.parse(validInput);
+    expect(parsed).toEqual(validInput);
+
+    expect(() => {
+      checkOffTodoList.inputSchema.parse({ todoItem: 123 });
+    }).toThrow();
+
+    expect(() => {
+      checkOffTodoList.inputSchema.parse({});
+    }).toThrow();
+  });
+
+  it('should validate output schema', () => {
+    const validOutput = {
+      success: true,
+      updatedTodoList: '- [x] Done',
+      message: 'Success',
+    };
+    const parsed = checkOffTodoList.outputSchema.parse(validOutput);
+    expect(parsed).toEqual(validOutput);
+
+    const minimalOutput = {
+      success: false,
+      updatedTodoList: '',
+    };
+    const minimalParsed = checkOffTodoList.outputSchema.parse(minimalOutput);
+    expect(minimalParsed).toEqual(minimalOutput);
+  });
+});
diff --git a/packages/ai/src/tools/planning-thinking-tools/check-off-todo-list-tool/check-off-todo-list-tool.ts b/packages/ai/src/tools/planning-thinking-tools/check-off-todo-list-tool/check-off-todo-list-tool.ts
new file mode 100644
index 000000000..d81e931c0
--- /dev/null
+++ b/packages/ai/src/tools/planning-thinking-tools/check-off-todo-list-tool/check-off-todo-list-tool.ts
@@ -0,0 +1,84 @@
+import type { RuntimeContext } from '@mastra/core/runtime-context';
+import { createTool } from '@mastra/core/tools';
+import { wrapTraced } from 'braintrust';
+import { z } from 'zod';
+import { type DocsAgentContext, DocsAgentContextKey } from '../../../context/docs-agent-context';
+
+const checkOffTodoListInputSchema = z.object({
+  todoItem: z.string().describe('The exact text of the todo item to check off in the list'),
+});
+
+const checkOffTodoListOutputSchema = z.object({
+  success: z.boolean(),
+  updatedTodoList: z.string().describe('The updated todo list with the item checked off'),
+  message: z.string().optional(),
+});
+
+const checkOffTodoListExecution = wrapTraced(
+  async (
+    params: z.infer<typeof checkOffTodoListInputSchema>,
+    runtimeContext: RuntimeContext<DocsAgentContext>
+  ): Promise<z.infer<typeof checkOffTodoListOutputSchema>> => {
+    const { todoItem } = params;
+
+    try {
+      // Get the current todo list from context
+      const currentTodoList = runtimeContext.get('todoList');
+
+      if (!currentTodoList) {
+        return {
+          success: false,
+          updatedTodoList: '',
+          message: 'No todo list found in context',
+        };
+      }
+
+      // Check if the item exists in the list (not already checked off)
+      if (!currentTodoList.includes(`- [ ] ${todoItem}`)) {
+        return {
+          success: false,
+          updatedTodoList: currentTodoList,
+          message: `Todo item "${todoItem}" not found in the list or already checked off`,
+        };
+      }
+
+      // Replace the unchecked item with a checked version
+      const updatedTodoList = currentTodoList.replace(`- [ ] ${todoItem}`, `- [x] ${todoItem}`);
+
+      // Update the context with the new todo list
+      runtimeContext.set('todoList', updatedTodoList);
+
+      return {
+        success: true,
+        updatedTodoList,
+        message: `Successfully checked off: "${todoItem}"`,
+      };
+    } catch (error) {
+      return {
+        success: false,
+        updatedTodoList: '',
+        message: `Error checking off todo item: ${error instanceof Error ? error.message : 'Unknown error'}`,
+      };
+    }
+  },
+  { name: 'check-off-todo-list' }
+);
+
+export const checkOffTodoList = createTool({
+  id: 'check-off-todo-list',
+  description:
+    'Check off a todo item in the todo list by replacing "- [ ]" with "- [x]". The todo list is maintained as a string in the runtime context.',
+  inputSchema: checkOffTodoListInputSchema,
+  outputSchema: checkOffTodoListOutputSchema,
+  execute: async ({
+    context,
+    runtimeContext,
+  }: {
+    context: z.infer<typeof checkOffTodoListInputSchema>;
+    runtimeContext: RuntimeContext<DocsAgentContext>;
+  }) => {
+    return await checkOffTodoListExecution(context, runtimeContext);
+  },
+});
+
+export default checkOffTodoList;
diff --git a/packages/ai/src/tools/planning-thinking-tools/update-clarifications-file-tool/update-clarifications-file-tool.test.ts b/packages/ai/src/tools/planning-thinking-tools/update-clarifications-file-tool/update-clarifications-file-tool.test.ts
new file mode 100644
index 000000000..a0f834dcd
--- /dev/null
+++ b/packages/ai/src/tools/planning-thinking-tools/update-clarifications-file-tool/update-clarifications-file-tool.test.ts
@@ -0,0 +1,187 @@
+import { RuntimeContext } from '@mastra/core/runtime-context';
+import { beforeEach, describe, expect, it } from 'vitest';
+import type { DocsAgentContext } from '../../../context/docs-agent-context';
+import { updateClarificationsFile } from './update-clarifications-file-tool';
+
+describe('updateClarificationsFile', () => {
+  let runtimeContext: RuntimeContext<DocsAgentContext>;
+
+  beforeEach(() => {
+    runtimeContext = new RuntimeContext<DocsAgentContext>();
+  });
+
+  it('should add a clarification question successfully', async () => {
+    const result = await updateClarificationsFile.execute({
+      context: {
+        issue: 'Database connection configuration',
+        context:
+          'The user mentioned they need to connect to a database but did not specify which type',
+        clarificationQuestion:
+          'Which type of database are you using? (PostgreSQL, MySQL, MongoDB, etc.)',
+      },
+      runtimeContext,
+    });
+
+    expect(result.success).toBe(true);
+    expect(result.clarification).toEqual({
+      issue: 'Database connection configuration',
+      context:
+        'The user mentioned they need to connect to a database but did not specify which type',
+      clarificationQuestion:
+        'Which type of database are you using? (PostgreSQL, MySQL, MongoDB, etc.)',
+    });
+    expect(result.message).toBe('Successfully added clarification question');
+
+    // Verify context was updated
+    const savedClarification = runtimeContext.get('clarificationQuestion');
+    expect(savedClarification).toEqual(result.clarification);
+  });
+
+  it('should overwrite previous clarification when adding new one', async () => {
+    // Add first clarification
+    await updateClarificationsFile.execute({
+      context: {
+        issue: 'First issue',
+        context: 'First context',
+        clarificationQuestion: 'First question?',
+      },
+      runtimeContext,
+    });
+
+    // Add second clarification
+    const result = await updateClarificationsFile.execute({
+      context: {
+        issue: 'Second issue',
+        context: 'Second context',
+        clarificationQuestion: 'Second question?',
+      },
+      runtimeContext,
+    });
+
+    expect(result.success).toBe(true);
+    expect(result.clarification).toEqual({
+      issue: 'Second issue',
+      context: 'Second context',
+      clarificationQuestion: 'Second question?',
+    });
+
+    // Verify only the second clarification is stored
+    const savedClarification = runtimeContext.get('clarificationQuestion');
+    expect(savedClarification).toEqual(result.clarification);
+  });
+
+  it('should handle very long clarification content', async () => {
+    const longText = 'A'.repeat(1000);
+
+    const result = await updateClarificationsFile.execute({
+      context: {
+        issue: longText,
+        context: longText,
+        clarificationQuestion: `${longText}?`,
+      },
+      runtimeContext,
+    });
+
+    expect(result.success).toBe(true);
+    expect(result.clarification?.issue).toBe(longText);
+    expect(result.clarification?.context).toBe(longText);
+    expect(result.clarification?.clarificationQuestion).toBe(`${longText}?`);
+  });
+
+  it('should validate input schema', () => {
+    const validInput = {
+      issue: 'Test issue',
+      context: 'Test context',
+      clarificationQuestion: 'Test question?',
+    };
+    const parsed = updateClarificationsFile.inputSchema.parse(validInput);
+    expect(parsed).toEqual(validInput);
+
+    // Missing required fields
+    expect(() => {
+      updateClarificationsFile.inputSchema.parse({
+        issue: 'Test issue',
+        context: 'Test context',
+      });
+    }).toThrow();
+
+    expect(() => {
+      updateClarificationsFile.inputSchema.parse({
+        issue: 'Test issue',
+        clarificationQuestion: 'Test question?',
+      });
+    }).toThrow();
+
+    expect(() => {
+      updateClarificationsFile.inputSchema.parse({
+        context: 'Test context',
+        clarificationQuestion: 'Test question?',
+      });
+    }).toThrow();
+
+    // Wrong types
+    expect(() => {
+      updateClarificationsFile.inputSchema.parse({
+        issue: 123,
+        context: 'Test context',
+        clarificationQuestion: 'Test question?',
+      });
+    }).toThrow();
+  });
+
+  it('should validate output schema', () => {
+    const validOutput = {
+      success: true,
+      clarification: {
+        issue: 'Test issue',
+        context: 'Test context',
+        clarificationQuestion: 'Test question?',
+      },
+      message: 'Success',
+    };
+    const parsed = updateClarificationsFile.outputSchema.parse(validOutput);
+    expect(parsed).toEqual(validOutput);
+
+    const minimalOutput = {
+      success: false,
+    };
+    const minimalParsed = updateClarificationsFile.outputSchema.parse(minimalOutput);
+    expect(minimalParsed).toEqual(minimalOutput);
+  });
+
+  it('should handle empty strings', async () => {
+    const result = await updateClarificationsFile.execute({
+      context: {
+        issue: '',
+        context: '',
+        clarificationQuestion: '',
+      },
+      runtimeContext,
+    });
+
+    expect(result.success).toBe(true);
+    expect(result.clarification).toEqual({
+      issue: '',
+      context: '',
+      clarificationQuestion: '',
+    });
+  });
+
+  it('should handle special characters in clarification content', async () => {
+    const result = await updateClarificationsFile.execute({
+      context: {
+        issue: 'Issue with "quotes" and \'apostrophes\'',
+        context: 'Context with\nnewlines\tand\ttabs',
+        clarificationQuestion: 'Question with émojis 🤔 and special chars: <>?/@#$%',
+      },
+      runtimeContext,
+    });
+
+    expect(result.success).toBe(true);
+    expect(result.clarification).toEqual({
+      issue: 'Issue with "quotes" and \'apostrophes\'',
+      context: 'Context with\nnewlines\tand\ttabs',
+      clarificationQuestion: 'Question with émojis 🤔 and special chars: <>?/@#$%',
+    });
+  });
+});
diff --git a/packages/ai/src/tools/planning-thinking-tools/update-clarifications-file-tool/update-clarifications-file-tool.ts b/packages/ai/src/tools/planning-thinking-tools/update-clarifications-file-tool/update-clarifications-file-tool.ts
new file mode 100644
index 000000000..71505fdb3
--- /dev/null
+++ b/packages/ai/src/tools/planning-thinking-tools/update-clarifications-file-tool/update-clarifications-file-tool.ts
@@ -0,0 +1,88 @@
+import type { RuntimeContext } from '@mastra/core/runtime-context';
+import { createTool } from '@mastra/core/tools';
+import { wrapTraced } from 'braintrust';
+import { z } from 'zod';
+import {
+  ClarifyingQuestionSchema,
+  type DocsAgentContext,
+  DocsAgentContextKey,
+  type MessageUserClarifyingQuestion,
+} from '../../../context/docs-agent-context';
+
+const updateClarificationsInputSchema = z.object({
+  issue: z.string().describe('The issue or problem that needs clarification'),
+  context: z
+    .string()
+    .describe('The context around the issue to help understand what clarification is needed'),
+  clarificationQuestion: z
+    .string()
+    .describe('The specific question to ask the user for clarification'),
+});
+
+const updateClarificationsOutputSchema = z.object({
+  success: z.boolean(),
+  clarification: ClarifyingQuestionSchema.optional(),
+  message: z.string().optional(),
+});
+
+const updateClarificationsExecution = wrapTraced(
+  async (
+    params: z.infer<typeof updateClarificationsInputSchema>,
+    runtimeContext: RuntimeContext<DocsAgentContext>
+  ): Promise<z.infer<typeof updateClarificationsOutputSchema>> => {
+    const { issue, context, clarificationQuestion } = params;
+
+    try {
+      // Create the new clarification question
+      const newClarification: MessageUserClarifyingQuestion = {
+        issue,
+        context,
+        clarificationQuestion,
+      };
+
+      // Validate the clarification against the schema
+      const validatedClarification = ClarifyingQuestionSchema.parse(newClarification);
+
+      // Update the context with the new clarification
+      runtimeContext.set('clarificationQuestion', validatedClarification);
+
+      return {
+        success: true,
+        clarification: validatedClarification,
+        message: 'Successfully added clarification question',
+      };
+    } catch (error) {
+      if (error instanceof z.ZodError) {
+        return {
+          success: false,
+          message: `Validation error: ${error.errors.map((e) => e.message).join(', ')}`,
+        };
+      }
+
+      return {
+        success: false,
+        message: `Error adding clarification: ${error instanceof Error ? error.message : 'Unknown error'}`,
+      };
+    }
+  },
+  { name: 'update-clarifications-file' }
+);
+
+export const updateClarificationsFile = createTool({
+  id: 'update-clarifications-file',
+  description:
+    'Add a new clarification question to the context. This tool helps agents request clarification from users when they encounter ambiguous or unclear requirements.',
+  inputSchema: updateClarificationsInputSchema,
+  outputSchema: updateClarificationsOutputSchema,
+  execute: async ({
+    context,
+    runtimeContext,
+  }: {
+    context: z.infer<typeof updateClarificationsInputSchema>;
+    runtimeContext: RuntimeContext<DocsAgentContext>;
+  }) => {
+    return await updateClarificationsExecution(context, runtimeContext);
+  },
+});
+
+export default updateClarificationsFile;