Please contact us at info@morphllm.com for access to the Morph Embeddings and Morph Reranking models.

Agent Tools for Code and File Manipulation

This guide explores the key tools available to AI agents for code and file manipulation, providing best practices for implementing and using these tools in your agent prompts.

Understanding Tool Architecture

Tools transform agents from conversational assistants to action-oriented systems. Effective agents require:

Clear tool definitions: Functions with precise descriptions and parameters
Usage protocols: Guidelines for when and how to use each tool
Error handling: Procedures for when tools don’t behave as expected

The Edit File Tool

The edit_file tool is the most critical tool for coding agents. It enables precise, fast modifications to any file in your codebase without requiring the reasoning agent to rewrite entire files.

How Edit File Works

The tool operates on a simple principle: show only what changes, mark everything else as unchanged. This approach:

Minimizes token usage by not repeating large unchanged sections
Reduces errors by providing clear context about what should change
Enables precise edits in large files without full rewrites
Works with any file type - code, configs, docs, anything

Key Concepts

Precision: Only specify the lines that need to change
Context Markers: Use // ... existing code ... to indicate unchanged sections
Clear Boundaries: Provide enough surrounding context for proper placement

Implementation Example

This example demonstrates how to create an edit_file tool that uses Morph’s fast apply API to modify files:

import { tool } from 'ai';
import { z } from 'zod';
import * as fs from 'fs/promises';
import { OpenAI } from 'openai';

const morphClient = new OpenAI({
  apiKey: process.env.MORPH_API_KEY,
  baseURL: 'https://api.morphllm.com/v1'
});

const editFile = tool({
  description: 
    'Edit a file by specifying only the lines that need to change. ' +
    'Use "// ... existing code ..." comments to represent unchanged sections. ' +
    'Provide enough context around changes for proper placement.',
  parameters: z.object({
    target_file: z.string().describe('Path to the file to edit'),
    instructions: z.string().describe('Brief description of what you are changing'),
    code_edit: z.string().describe(
      'The edit content with "// ... existing code ..." markers for unchanged sections'
    ),
  }),
  execute: async ({ target_file, instructions, code_edit }) => {
    try {
      // Read the current file content
      const originalCode = await fs.readFile(target_file, 'utf-8');
      
      // Use Morph's fast apply API to generate the updated code
      const response = await morphClient.chat.completions.create({
        model: "morph-v2",
        messages: [
          {
            role: "user",
            content: `<code>${originalCode}</code>\n<update>${code_edit}</update>`
          }
        ],
        stream: false // set to true if you want to stream the response
      });
      
      const updatedCode = response.choices[0].message.content;
      
      // Write the updated content back to the file
      await fs.writeFile(target_file, updatedCode, 'utf-8');
      
      return {
        success: true,
        message: `Successfully applied edit to ${target_file}: ${instructions}`,
        changes_applied: code_edit
      };
    } catch (error) {
      return {
        success: false,
        error: `Failed to edit ${target_file}: ${error.message}`
      };
    }
  },
});

Edit Format Examples

JavaScript/TypeScript files:

// ... existing code ...
function calculateTotal(items) {
  return items.reduce((total, item) => {
    // Add tax calculation
    const tax = item.price * 0.08;
    return total + item.price + tax;
  }, 0);
}
// ... existing code ...

Python files:

# ... existing code ...
def calculate_total(items):
    total = 0
    for item in items:
        // Add tax calculation
        tax = item.price * 0.08
        total += item.price + tax
    return total
# ... existing code ...

Best Practices

Read before you edit: Always examine the file first to understand its structure
Minimal changes: Only include the lines that actually need modification
Sufficient context: Include enough surrounding lines for unambiguous placement
Language-appropriate comments: Use the correct comment syntax for each file type
Clear instructions: Provide concise descriptions of what you’re changing

Common Patterns

Adding new code:

// ... existing code ...
export function newFunction() {
  return "This is new functionality";
}
// ... existing code ...

Modifying existing code:

// ... existing code ...
function existingFunction() {
  // Updated implementation
  return "Modified behavior";
}
// ... existing code ...

Multiple changes in sequence:

// ... existing code ...
const FIRST_CHANGE = "new value";
// ... existing code ...
function secondChange() {
  return "updated function";
}
// ... existing code ...
const THIRD_CHANGE = "another new value";
// ... existing code ...

Core File Manipulation Tools

read_file: Building Context Awareness

Before editing files, agents need context about existing code:

{
  "name": "read_file",
  "description": "Read the contents of a file. the output of this tool call will be the 1-indexed file contents from start_line_one_indexed to end_line_one_indexed_inclusive, together with a summary of the lines outside start_line_one_indexed and end_line_one_indexed_inclusive.\nNote that this call can view at most 250 lines at a time.\n\nWhen using this tool to gather information, it's your responsibility to ensure you have the COMPLETE context. Specifically, each time you call this command you should:\n1) Assess if the contents you viewed are sufficient to proceed with your task.\n2) Take note of where there are lines not shown.\n3) If the file contents you have viewed are insufficient, and you suspect they may be in lines not shown, proactively call the tool again to view those lines.\n4) When in doubt, call this tool again to gather more information. Remember that partial file views may miss critical dependencies, imports, or functionality.\n\nIn some cases, if reading a range of lines is not enough, you may choose to read the entire file.\nReading entire files is often wasteful and slow, especially for large files (i.e. more than a few hundred lines). So you should use this option sparingly.\nReading the entire file is not allowed in most cases. You are only allowed to read the entire file if it has been edited or manually attached to the conversation by the user.",
  "parameters": {
    "properties": {
      "relative_workspace_path": "The path of the file to read, relative to the workspace root.",
      "start_line_one_indexed": "The one-indexed line number to start reading from (inclusive).",
      "end_line_one_indexed_inclusive": "The one-indexed line number to end reading at (inclusive).",
      "should_read_entire_file": "Whether to read the entire file. Defaults to false.",
      "explanation": "One sentence explanation as to why this tool is being used, and how it contributes to the goal."
    },
    "required": ["relative_workspace_path", "should_read_entire_file", "start_line_one_indexed", "end_line_one_indexed_inclusive"]
  }
}

Best practices:

Read before you edit - always obtain context before making changes
Start with targeted reads of relevant sections (lines)
Progress to larger context if initial reads are insufficient
When reading complex code, follow imports and references to build complete understanding

codebase_search: Finding Relevant Code

Semantic search helps agents understand large codebases:

{
  "name": "codebase_search",
  "description": "Find snippets of code from the codebase most relevant to the search query.\nThis is a semantic search tool, so the query should ask for something semantically matching what is needed.\nIf it makes sense to only search in particular directories, please specify them in the target_directories field.\nUnless there is a clear reason to use your own search query, please just reuse the user's exact query with their wording.\nTheir exact wording/phrasing can often be helpful for the semantic search query. Keeping the same exact question format can also be helpful.",
  "parameters": {
    "properties": {
      "query": "The search query to find relevant code. You should reuse the user's exact query/most recent message with their wording unless there is a clear reason not to.",
      "target_directories": "Glob patterns for directories to search over",
      "explanation": "One sentence explanation as to why this tool is being used, and how it contributes to the goal."
    },
    "required": ["query"]
  }
}

You should use Morph Embeddings and Morph Reranking to implement the codebase_search tool.

Best practices:

Prefer to use the user’s query wording for better semantic matching
Start with broad searches, then refine based on results
Use for understanding concepts, patterns or functions in unfamiliar code

list_dir: Directory Exploration

Helps agents understand project structure:

{
  "name": "list_dir",
  "description": "List the contents of a directory. The quick tool to use for discovery, before using more targeted tools like semantic search or file reading. Useful to try to understand the file structure before diving deeper into specific files. Can be used to explore the codebase.",
  "parameters": {
    "properties": {
      "relative_workspace_path": "Path to list contents of, relative to the workspace root.",
      "explanation": "One sentence explanation as to why this tool is being used, and how it contributes to the goal."
    },
    "required": ["relative_workspace_path"]
  }
}

Best practices:

Start exploration with high-level directory listing
Use as an initial discovery step before deeper analysis
Build a mental map of project structure before diving into code

file_search: Filename Discovery

Use when you need to locate files by name or pattern:

{
  "name": "file_search",
  "description": "Fast file search based on fuzzy matching against file path. Use if you know part of the file path but don't know where it's located exactly. Response will be capped to 10 results. Make your query more specific if need to filter results further.",
  "parameters": {
    "properties": {
      "query": "Fuzzy filename to search for",
      "explanation": "One sentence explanation as to why this tool is being used, and how it contributes to the goal."
    },
    "required": ["query", "explanation"]
  }
}

Best practices:

Use when you know part of a filename but not its location
Make queries specific to filter results when needed
Combine with directory exploration for effective navigation

Advanced Tools

grep_search: Pattern Matching

When you need exact matches rather than semantic search:

{
  "name": "grep_search",
  "description": "Fast text-based regex search that finds exact pattern matches within files or directories, utilizing the ripgrep command for efficient searching.\nResults will be formatted in the style of ripgrep and can be configured to include line numbers and content.\nTo avoid overwhelming output, the results are capped at 50 matches.\nUse the include or exclude patterns to filter the search scope by file type or specific paths.\n\nThis is best for finding exact text matches or regex patterns.\nMore precise than semantic search for finding specific strings or patterns.\nThis is preferred over semantic search when we know the exact symbol/function name/etc. to search in some set of directories/file types.",
  "parameters": {
    "properties": {
      "query": "The regex pattern to search for",
      "case_sensitive": "Whether the search should be case sensitive",
      "include_pattern": "Glob pattern for files to include (e.g. '*.ts' for TypeScript files)",
      "exclude_pattern": "Glob pattern for files to exclude",
      "explanation": "One sentence explanation as to why this tool is being used, and how it contributes to the goal."
    },
    "required": ["query"]
  }
}

Best practices:

Use for finding function declarations, variable usages, or specific patterns
Combine with codebase_search for comprehensive discovery
Use specific patterns to avoid overwhelming results

run_terminal_cmd: Executing Commands

Execute commands to interact with the system:

{
  "name": "run_terminal_cmd",
  "description": "PROPOSE a command to run on behalf of the user.\nIf you have this tool, note that you DO have the ability to run commands directly on the USER's system.\nNote that the user will have to approve the command before it is executed.\nThe user may reject it if it is not to their liking, or may modify the command before approving it. If they do change it, take those changes into account.\nThe actual command will NOT execute until the user approves it. The user may not approve it immediately. Do NOT assume the command has started running.\nIf the step is WAITING for user approval, it has NOT started running.\nIn using these tools, adhere to the following guidelines:\n1. Based on the contents of the conversation, you will be told if you are in the same shell as a previous step or a different shell.\n2. If in a new shell, you should cd to the appropriate directory and do necessary setup in addition to running the command.\n3. If in the same shell, the state will persist (eg. if you cd in one step, that cwd is persisted next time you invoke this tool).\n4. For ANY commands that would use a pager or require user interaction, you should append  | cat to the command (or whatever is appropriate). Otherwise, the command will break. You MUST do this for: git, less, head, tail, more, etc.\n5. For commands that are long running/expected to run indefinitely until interruption, please run them in the background. To run jobs in the background, set is_background to true rather than changing the details of the command.\n6. Dont include any newlines in the command.",
  "parameters": {
    "properties": {
      "command": "The terminal command to execute",
      "explanation": "One sentence explanation as to why this command needs to be run and how it contributes to the goal.",
      "is_background": "Whether the command should be run in the background",
      "require_user_approval": "Whether the user must approve the command before it is executed. Only set this to true if the command is safe and if it matches the user's requirements for commands that should be executed automatically."
    },
    "required": ["command", "is_background", "require_user_approval"]
  }
}

Best practices:

Always include proper explanations for commands
Use the pipe to cat for any commands that would use a pager
Set background flag for long-running operations
Consider the current shell context when running commands

parallel_apply: Systematic Changes

For consistent changes across multiple files:

{
  "name": "parallel_apply",
  "description": "When there are multiple locations that can be edited in parallel, with a similar type of edit, use this tool to sketch out a plan for the edits.\nYou should start with the edit_plan which describes what the edits will be.\nThen, write out the files that will be edited with the edit_files argument.\nYou shouldn't edit more than 50 files at a time.",
  "parameters": {
    "properties": {
      "edit_plan": "A detailed description of the parallel edits to be applied.\nThey should be specified in a way where a model just seeing one of the files and this plan would be able to apply the edits to any of the files.\nIt should be in the first person, describing what you will do on another iteration, after seeing the file.",
      "edit_regions": {
        "items": {
          "properties": {
            "relative_workspace_path": "The path to the file to edit.",
            "start_line": "The start line of the region to edit. 1-indexed and inclusive.",
            "end_line": "The end line of the region to edit. 1-indexed and inclusive."
          },
          "required": ["relative_workspace_path"]
        },
        "type": "array"
      }
    },
    "required": ["edit_plan", "edit_regions"]
  }
}

Best practices:

Use for refactoring, renaming, or pattern application
Create clear edit plans that could be applied independently
Provide sufficient context in edit regions

reapply: Error Recovery

When edits don’t apply correctly:

{
  "name": "reapply",
  "description": "Calls a smarter model to apply the last edit to the specified file.\nUse this tool immediately after the result of an edit_file tool call ONLY IF the diff is not what you expected, indicating the model applying the changes was not smart enough to follow your instructions.",
  "parameters": {
    "properties": {
      "target_file": "The relative path to the file to reapply the last edit to."
    },
    "required": ["target_file"]
  }
}

Best practices:

Only use after a failed edit_file attempt
Examine what went wrong with the initial attempt
Consider simplifying the edit if reapply also fails

delete_file: File Removal

Remove files from the workspace:

{
  "name": "delete_file",
  "description": "Deletes a file at the specified path. The operation will fail gracefully if:\n - The file doesn't exist\n - The operation is rejected for security reasons\n - The file cannot be deleted",
  "parameters": {
    "properties": {
      "target_file": "The path of the file to delete, relative to the workspace root.",
      "explanation": "One sentence explanation as to why this tool is being used, and how it contributes to the goal."
    },
    "required": ["target_file"]
  }
}

Best practices:

Always include clear explanations for file deletions
Verify the file exists before attempting deletion
Consider creating backups before deletion when appropriate

Tool Usage Workflow

Effective coding agents typically follow this tool usage pattern:

Discovery: Use list_dir to understand project structure
Search: Use codebase_search or grep_search to find relevant code - Use Morph Embeddings and Morph Reranking to implement the tools - contact info@morphllm.com for access
Context Building: Use read_file to examine important sections
Modification: Use edit_file to make precise changes
Verification: Use read_file again to verify changes were applied correctly

Tool Prompting Guidelines

When implementing tools in your agent prompts:

Clear function definitions: Provide comprehensive JSONSchema definitions
Usage protocols: Define when and how each tool should be used
Error handling: Include procedures for tool failures
Context management: Guide the agent to build sufficient context before actions
Progressive approach: Start with discovery, then focused understanding, then action

Common Tool Anti-patterns

Avoid these common mistakes in agent tool implementations:

Insufficient context: Editing without fully understanding the code
Over-verbosity: Including too much unchanged code in edits
Premature editing: Making changes before properly exploring the codebase
Context fragmentation: Reading small disconnected sections without building overall understanding
Ignoring error recovery: Not implementing fallbacks when tools fail

Conclusion

Effective tool usage transforms AI agents from passive assistants to active agentic partners. By combining comprehensive tool definitions with clear usage protocols and error handling procedures, you can create agents that navigate, understand, and modify code with high accuracy and efficiency.

Getting Started

Models

Guides

Endpoints

Agent Tools

Agent Tools for Code and File Manipulation

Understanding Tool Architecture

The Edit File Tool

How Edit File Works

Key Concepts

Edit Format Examples

Best Practices

Common Patterns

Core File Manipulation Tools

Discovery and Navigation Tools

Advanced Tools

Tool Usage Workflow

Tool Prompting Guidelines

Common Tool Anti-patterns

Conclusion

Getting Started

Models

Guides

Endpoints

​Agent Tools for Code and File Manipulation

​Understanding Tool Architecture

​The Edit File Tool

​How Edit File Works

​Key Concepts

​Edit Format Examples

​Best Practices

​Common Patterns

​Core File Manipulation Tools

​Discovery and Navigation Tools

​Advanced Tools

​Tool Usage Workflow

​Tool Prompting Guidelines

​Common Tool Anti-patterns

​Conclusion

Agent Tools for Code and File Manipulation

Understanding Tool Architecture

The Edit File Tool

How Edit File Works

Key Concepts

Edit Format Examples

Best Practices

Common Patterns

Core File Manipulation Tools

Discovery and Navigation Tools

Advanced Tools

Tool Usage Workflow

Tool Prompting Guidelines

Common Tool Anti-patterns

Conclusion