Claude Command Runner

A powerful Model Context Protocol (MCP) server that bridges Claude Desktop and Warp's native agent panel with terminal applications. v6.0 adds dual-consumer support: the same binary serves both Claude Desktop and Warp's built-in agent. 39 integrated tools.

🚀 What's New in v6.0.0 — Warp re-pivot

Triggered by Warp going open source under AGPL-3.0 (github.com/warpdotdev/warp) in May 2026. v6.0 re-establishes Warp as the primary integration target and adds a new install path: Warp's native agent panel.

Dual-consumer architecture: register claude-command-runner in ~/.warp/.mcp.json and Warp's built-in agent (which uses your configured LLM — Claude Sonnet, Opus, etc.) calls the same tools Claude Desktop calls. Same binary, same code, two consumers. See docs/WARP_AGENT.md.
Deeplinks replace AppleScript for tab/window operations: open_terminal_tab now uses warp://action/new_tab?path=.... No menu-clicking, no Accessibility permission for the open path.
OSC 777 emitter (emit_warp_event): build printf invocations that surface structured events into Warp's notification UI. Schema reimplemented from upstream event/v1.rs (no vendoring).
Workspace profiles → Warp launch configs: save_workspace_profile accepts include_warp_launch_config: true to also write a YAML to ~/.warp/launch_configurations/, making the profile appear in Warp's launch UI.
Optional shell shim (Tier E, opt-in): helper/install-shim.sh adds zsh/bash hooks that emit preexec/command_finished events to a per-uid Unix socket the MCP listens on. Auto-disables outside Warp panes. Observability surface in v6.0; auto-routing execute_command through it is deferred to v6.0.x.
Cleanup: ~460 LOC of dead code removed (obsolete Warp DB integration, orphan TCP listener, unreachable background monitor). Tool count corrected: README claimed 30, reality was 36, v6.0 ships 39.
Reproducible build: swift-sdk pinned to 0.10.x with a deterministic scripts/patch-swift-sdk.sh so a fresh clone builds without manual patches.

Honest caveat: the "Claude" replying in Warp's agent panel is Warp's agent (running whichever LLM you configure in Warp's AI settings), not your Claude Desktop instance. Both can call the MCP; they don't share conversations. v6.0 does not bridge them.

What's New in v5.0.0 (history)

v5.0.0: 36 tools, up from 12.

Clipboard Bridge: Read from and write to the macOS clipboard without leaving the conversation
macOS Notifications: Get native notifications when long-running commands finish
Environment Intelligence: Probe your terminal context (git branch, active venv, Node version, Docker containers) in one call
Output Parsers: Structured JSON parsing for git status, docker ps, test results, and more
Environment Snapshots: Capture and diff environment variables before/after installs or config changes
Workspace Profiles: Save and restore project contexts (directory, env vars, common commands) per project
Multi-Terminal Sessions: Open, name, and send commands to multiple terminal tabs
Interactive Command Detection: Smart detection of interactive commands (vim, ssh, python REPL) with graceful handling
File System Watchers: Watch directories for changes and trigger commands automatically
SSH Remote Execution: Run commands on remote hosts via SSH key authentication

Previous Releases (Included)

v4.0: Command pipelines, output streaming, reusable templates
v3.0: Smart auto-retrieve, SQLite history, configurable security

Overview

Claude Command Runner is a dual-consumer MCP server — the same binary serves Claude Desktop and Warp's native agent panel. It enables an LLM (whichever you've configured in either client) to:

Execute terminal commands directly from conversations
Chain commands with conditional logic using pipelines
Stream output in real-time for long builds
Save and reuse command templates with variables
Automatically capture output with intelligent timing
Track command history and patterns
Read/write the macOS clipboard
Probe environment context (git, venv, Docker, Node)
Parse command output into structured JSON
Manage workspace profiles per project (with optional emission as Warp launch configs)
Orchestrate multiple terminal tabs (open via warp:// deeplinks; AppleScript fallback for non-Warp terminals)
Watch files and trigger commands on changes
Execute commands on remote hosts via SSH
(v6.0) Surface tool-execution status to Warp's UI as OSC 777 warp://cli-agent events
(v6.0, opt-in) Stream clean preexec / command-finished events from your shell to the MCP via a per-uid Unix domain socket

🎯 Key Features

Command Pipelines

Chain multiple commands with intelligent failure handling:

{
  "steps": [
    {"name": "Build", "command": "swift build", "on_fail": "stop"},
    {"name": "Test", "command": "swift test", "on_fail": "continue"},
    {"name": "Package", "command": "swift build -c release", "on_fail": "stop"}
  ]
}

Failure modes:

stop – Halt pipeline on failure
continue – Log error and proceed to next step
warn – Show warning and continue

Output Streaming

Real-time output for long-running commands:

{
  "command": "swift build -c release",
  "update_interval": 3,
  "max_duration": 180
}

Perfect for:

Long compilation processes
Test suites
Any command that previously "hung" waiting for output

Command Templates

Save reusable patterns with variable substitution:

// Save a template
{
  "name": "swift-release",
  "template": "cd {{project}} && swift build -c release",
  "category": "Swift Development",
  "description": "Build Swift project in release mode"
}

// Run with variables
{
  "name": "swift-release",
  "variables": {"project": "~/GitHub/MyApp"}
}

Templates are stored in ~/.claude-command-runner/templates.json and persist across sessions.

Smart Auto-Retrieve

The execute_with_auto_retrieve command intelligently detects command types and adjusts wait times:

Quick commands (echo, pwd): 2-6 seconds
Moderate commands (git, npm): up to 20 seconds
Build commands (swift build, make): up to 77 seconds
Test commands: up to 40 seconds

📊 Why Warp Terminal?

Warp Terminal is the primary integration target. The other terminals work for the basics — what Warp uniquely unlocks in v6.0 is documented integration surfaces:

Feature	Warp	Terminal.app	iTerm2
`warp://` deeplinks for tab/window	✅ (v6.0 uses these)	❌	❌
Native MCP agent panel — chat with Claude in the terminal	✅ (`~/.warp/.mcp.json`)	❌	❌
OSC 777 cli-agent event channel for status surfacing	✅	❌	❌
Workspace profile → recognized launch config	✅ (`~/.warp/launch_configurations/`)	❌	❌
AppleScript-driven new tab + keystroke send	✅	✅	✅
Modern UI/UX	✅	⚠️	⚠️

Output capture (/tmp/<id>.json polling) and the 24 tools that don't touch the terminal at all (clipboard, SSH, file watch, env snapshots, etc.) work identically across all terminals.

💡 Get Warp: Download Warp Terminal – it's free, open source (AGPL-3.0), and makes the v6.0-specific surfaces above available to you.

Installation

Prerequisites

macOS 13.0 or later
Swift 6.0+ (Xcode 16+)
Claude Desktop
A supported terminal (Warp strongly recommended)

Quick Install

Clone and build:

git clone https://github.com/M-Pineapple/claude-command-runner.git
cd claude-command-runner
./build.sh

Pick your consumer(s) — you can install for one or both:

A — Claude Desktop (~/Library/Application Support/Claude/claude_desktop_config.json):

{
  "mcpServers": {
    "claude-command-runner": {
      "command": "/path/to/claude-command-runner/.build/release/claude-command-runner",
      "args": []
    }
  }
}

B — Warp's native agent (~/.warp/.mcp.json):

{
  "mcpServers": {
    "claude-command-runner": {
      "command": "/path/to/claude-command-runner/.build/release/claude-command-runner",
      "args": []
    }
  }
}

See docs/WARP_AGENT.md for the full guide.

Grant Accessibility permission (only required for send_to_session keystroke injection in v6.0; tab/window opening uses deeplinks and does not require it):
- Open System Settings → Privacy & Security → Accessibility
- Click + and navigate to claude-command-runner/.build/release/
- Press Cmd+Shift+. to reveal the hidden .build folder
- Select the claude-command-runner binary and toggle it on

Important: macOS tracks permissions by binary identity. After every rebuild (./build.sh), you must remove the old entry and re-add the new binary in Accessibility settings.

Restart your client(s) (Claude Desktop and/or Warp).
(Optional) Install the shell shim for cleaner block-boundary capture:
```
helper/install-shim.sh
```
See helper/shell-shim.zsh / helper/shell-shim.bash for the implementation. Uninstall with helper/uninstall-shim.sh.

Usage

Available Tools (39)

Core Execution

Tool	Description	Use Case
`execute_command`	Execute with manual output retrieval	Simple commands
`execute_with_auto_retrieve`	Execute with intelligent auto-retrieval	Most common usage ⭐
`execute_pipeline`	Chain commands with conditional logic	Build workflows, CI/CD
`execute_with_streaming`	Real-time output streaming	Long builds, test suites
`save_template`	Save reusable command pattern	Create shortcuts
`run_template`	Execute saved template with variables	Run saved patterns
`list_templates`	View all saved templates	Manage templates
`get_command_output`	Manually retrieve command output	Debugging
`preview_command`	Preview without executing	Safety check
`suggest_command`	Get command suggestions	Discovery
`list_recent_commands`	View command history	Analytics
`self_check`	System health diagnostics	Troubleshooting

Clipboard (v5.0)

Tool	Description	Use Case
`copy_to_clipboard`	Write text to macOS clipboard	Share output
`read_from_clipboard`	Read current clipboard content	Paste context

Notifications (v5.0)

Tool	Description	Use Case
`set_notification_preference`	Toggle macOS notifications	Personalisation

Environment Intelligence (v5.0)

Tool	Description	Use Case
`get_environment_context`	Probe git, venv, Node, Docker state	Context awareness
`execute_and_parse`	Execute and parse output to structured JSON	Smart output
`capture_environment`	Snapshot all environment variables	Before/after comparison
`diff_environment`	Compare two environment snapshots	Change detection

Workspace Profiles (v5.0)

Tool	Description	Use Case
`save_workspace_profile`	Save project context as named profile	Project switching
`load_workspace_profile`	Restore a saved project context	Resume work
`list_workspace_profiles`	View all saved profiles	Organisation
`delete_workspace_profile`	Remove a workspace profile	Cleanup

Multi-Terminal Sessions (v5.0)

Tool	Description	Use Case
`open_terminal_tab`	Open a new named terminal tab (Warp: via `warp://action/new_tab` deeplink in v6.0)	Parallel workflows
`send_to_session`	Send command to a specific tab (AppleScript keystroke; tab-targeting limited on Warp)	Targeted execution
`list_sessions`	View active terminal sessions	Session overview
`close_session`	Close a named session	Cleanup
`cleanup_sessions`	Bulk-remove stale sessions; optionally close their tabs	Hygiene

Interactive Command Detection (v5.0)

Tool	Description	Use Case
`check_interactive`	Classify a command for TTY/stdin requirements before running it	Avoid hangs from `vim`, `ssh`, `psql`, REPLs

File Watching (v5.0)

Tool	Description	Use Case
`add_file_watch`	Watch directory and trigger command on changes	Auto-rebuild, auto-test
`remove_file_watch`	Stop watching a directory	Cleanup
`list_file_watches`	View active watchers	Overview

SSH Remote Execution (v5.0)

Tool	Description	Use Case
`ssh_execute`	Run command on remote host via SSH	Remote ops
`save_ssh_profile`	Save SSH connection profile	Quick connect
`list_ssh_profiles`	View saved SSH profiles	Overview
`delete_ssh_profile`	Remove an SSH profile	Cleanup

Warp v6.0 — deeplinks, OSC 777, shell shim

Tool	Description	Use Case
`focus_warp_session`	Dispatch `warp://session/<uuid>` to focus a Warp pane (UUID must be one Warp recognises — typically from the optional shell shim's events)	Resume work in a specific pane
`emit_warp_event`	Build a `printf` invocation that emits an OSC 777 `warp://cli-agent` JSON event into Warp's UI. Schema: `session_start` / `prompt_submit` / `tool_complete` / `stop` / `permission_request` / `idle_prompt`. The returned `printf` must be run inside a Warp pane (e.g. via `execute_command`) to take effect	Status notifications
`shell_shim_status`	Report optional shell-shim socket state and recent events	Verify shim is wired up

Example Workflows

Simple Command:

You: "Check my Swift version"
Claude: [execute_with_auto_retrieve: swift --version]
Claude: "You're running Swift 6.0.2"

Build Pipeline:

You: "Build, test, and package my app"
Claude: [execute_pipeline with build → test → package steps]
Claude: "Pipeline complete! Build: ✅ Test: ✅ Package: ✅"

Streaming Long Build:

You: "Build this large project"
Claude: [execute_with_streaming: swift build -c release]
Claude: "Building... [live updates every 3 seconds]"
Claude: "Build completed in 45 seconds!"

Using Templates:

You: "Save a template for deploying to staging"
Claude: [save_template: name="deploy-staging", template="cd {{project}} && ./deploy.sh staging"]

You: "Deploy MyApp to staging"
Claude: [run_template: name="deploy-staging", variables={project: "MyApp"}]

Environment Context (v5.0):

You: "What's my current dev environment?"
Claude: [get_environment_context]
Claude: "You're on branch feature/auth, Python venv active, Node 20.11, 3 Docker containers running."

Workspace Profiles (v5.0):

You: "Save this as my API project profile"
Claude: [save_workspace_profile: name="api-project", directory="~/Projects/api", ...]

You: "Switch to the API project"
Claude: [load_workspace_profile: name="api-project"]

File Watching (v5.0):

You: "Rebuild whenever a Swift file changes"
Claude: [add_file_watch: path="./Sources", pattern="*.swift", command="swift build"]
Claude: "Watching ./Sources for *.swift changes. Will run swift build on each change."

SSH Remote Execution (v5.0):

You: "Check disk space on the staging server"
Claude: [ssh_execute: host="staging.example.com", username="deploy", command="df -h"]
Claude: "Here's the disk usage on staging..."

Configuration

The configuration file is located at ~/.claude-command-runner/config.json:

{
  "terminal": {
    "preferred": "auto",
    "fallbackOrder": ["Warp", "WarpPreview", "iTerm", "Terminal"]
  },
  "security": {
    "blockedCommands": ["rm -rf /", "format"],
    "maxCommandLength": 1000
  },
  "history": {
    "enabled": true,
    "maxEntries": 10000
  },
  "notifications": {
    "enabled": true,
    "soundEnabled": true,
    "showOnSuccess": false,
    "showOnFailure": true,
    "minimumDuration": 10
  },
  "fileWatching": {
    "maxWatchers": 5,
    "defaultDebounce": 2.0,
    "autoExpireMinutes": 60
  },
  "ssh": {
    "defaultTimeout": 30,
    "allowPasswordAuth": false
  },
  "interactiveDetection": {
    "enabled": true,
    "customPatterns": []
  }
}

Templates are stored separately at ~/.claude-command-runner/templates.json.
Workspace profiles are stored at ~/.claude-command-runner/profiles.json.
SSH profiles are stored at ~/.claude-command-runner/ssh_profiles.json.

🤔 Frequently Asked Questions

Q: What's new in v6.0.0?

A: Re-pivot to Warp after Warp went open source. Dual-consumer architecture (register the same binary in ~/.warp/.mcp.json to use it from Warp's native agent panel, in addition to Claude Desktop). warp:// deeplinks replace AppleScript menu-clicking for tab/window operations. New OSC 777 emitter (emit_warp_event) surfaces structured events into Warp's UI. New optional shell shim emits clean preexec/command-finished events to the MCP. Workspace profiles can now also emit Warp-native launch configs. ~460 LOC of dead code removed. Tool count goes from a previously-undercounted 36 (the v5 README claimed 30) up to 39. See CHANGELOG.md and docs/WARP_AGENT.md for the full story.

Q: What was new in v5.0.0?

A: Ten new feature categories bringing the tool count from 12 to 36 (the v5 README under-counted as 30; the dispatch table actually registered 36). Highlights: clipboard integration, macOS notifications, environment intelligence, structured output parsing, workspace profiles, multi-terminal sessions, file watchers, SSH remote execution.

Q: When should I use pipelines vs regular commands?

A: Use pipelines when you need:

Multiple sequential commands
Conditional logic (stop on build failure, continue on test failure)
A summary of all steps with timing
CI/CD-style workflows

Q: Why does my command "hang" with execute_with_auto_retrieve?

A: For very long commands, use execute_with_streaming instead. It provides real-time output updates and handles commands that run for minutes. This was the main motivation for adding streaming in v4.0.

Q: How do I use templates with multiple variables?

A: Define variables in your template with {{variable_name}} syntax:

{
  "template": "cd {{project}} && git checkout {{branch}} && swift build -c {{config}}"
}

Then provide all variables when running:

{
  "variables": {"project": "~/MyApp", "branch": "main", "config": "release"}
}

Q: Where are my templates stored?

A: In ~/.claude-command-runner/templates.json. They persist across sessions and Claude Desktop restarts.

Q: How long will auto-retrieve wait for my command?

A: It depends on the command type:

Simple commands: 6 seconds
Git/npm commands: 20 seconds
Build commands: 77 seconds
Unknown commands: 30 seconds

For longer commands, use execute_with_streaming instead.

Q: Can I use this with Terminal.app or iTerm2?

A: Yes, basic command execution works with any terminal. However, automatic output capture and advanced features require Warp Terminal. Get Warp free here.

Q: Is it secure to let Claude run commands?

A: Commands are sent directly to your terminal and execute automatically — there is no manual "press Enter" step. However, you can configure blocked commands and patterns in the config file to prevent dangerous operations. Always review the command Claude proposes before confirming in the chat interface.

Q: What happens if a pipeline step fails?

A: Depends on the on_fail setting:

stop – Pipeline halts immediately, remaining steps are skipped
continue – Error is logged, pipeline continues to next step
warn – Warning is shown, pipeline continues

Q: Can I nest pipelines or run templates inside pipelines?

A: Not directly. You can create templates that contain multiple commands separated by && or ;, or compose by calling run_template and execute_pipeline from the same conversation.

Q: Where is my command history stored?

A: In an SQLite database at ~/.claude-command-runner/claude_commands.db. It tracks all commands, outputs, exit codes, and execution times.

🛠️ Troubleshooting

macOS Permission Error: "osascript is not allowed to send keystrokes" (Error 1002)

This error occurs when macOS blocks AppleScript automation. It's common after fresh macOS installs, major updates (like Sequoia), or when the Automation permissions cache becomes corrupted.

Symptoms:

Error message: System Events got an error: osascript is not allowed to send keystrokes. (1002)
Toggling permissions off/on in System Settings doesn't help
No permission prompt appears when the MCP tries to run

Solution:

Reset Automation permissions (this resets ALL Automation permissions, not just for this app):
```
tccutil reset AppleEvents
```
Full Mac restart (not just logout – a complete restart is required)
Open your terminal app first (Warp, WarpPreview, or whichever you use)
Open Claude Desktop

Trigger the permission prompt manually by running this in Terminal:

osascript -e 'tell application "System Events" to keystroke "x"'

Grant permission when macOS prompts you
Try the MCP command again – it should now work and Claude.app will appear in the Automation list

Note: A simple toggle reset or targeted tccutil command often doesn't work – the full AppleEvents reset plus restart is usually required.

Bundle ID Reference: Claude Desktop uses com.anthropic.claudefordesktop

macOS Accessibility Permission Issues

The MCP binary requires Accessibility permission only for the AppleScript keystroke path used by send_to_session (typing into a specific Warp tab) and the legacy non-Warp paths in execute_command for iTerm/Terminal/Alacritty. Most v6.0 tools work without Accessibility: subprocess-based execution, warp:// deeplinks for tab opening, clipboard, SSH, env snapshots, file watch, profiles, and all 24 server-side tools.

Symptoms (when it does matter):

Error message: osascript is not allowed assistive access. (-1719)
send_to_session fails; clipboard, SSH, env-context, deeplink-based open_terminal_tab all work fine

Solution:

Open System Settings → Privacy & Security → Accessibility

Click the + button and navigate to your claude-command-runner binary:

/path/to/claude-command-runner/.build/release/claude-command-runner

The .build folder is hidden by default — press Cmd+Shift+. in Finder to reveal it
Toggle the permission on for the binary

Important: macOS tracks Accessibility permissions by binary identity. After every swift build, the binary changes and you must re-add it to the Accessibility list. This only affects keystroke-injection paths — most tools are unaffected.

MCP Not Responding

Check the client logs (Claude Desktop or Warp). The MCP server runs as a child of the client over stdio — there is no listening TCP port in v6.0.
Restart the client (Claude Desktop and/or Warp).
Rebuild with ./build.sh. (And re-add the binary to Accessibility if send_to_session is failing.)

Commands Not Appearing in Terminal

Ensure Warp/WarpPreview is running
Check Claude Desktop logs for errors
Verify your MCP configuration path

Streaming Not Updating

Check that the command is actually running (not waiting for input)
Increase update_interval if updates are too frequent
Check /tmp/claude_stream_*.log for output files

Pipeline Steps Skipped Unexpectedly

Check the on_fail setting – stop will skip remaining steps
Verify each command works individually first
Check exit codes in the pipeline summary

Templates Not Saving

Ensure ~/.claude-command-runner/ directory exists
Check write permissions on templates.json
Verify JSON syntax in template definition

Auto-Retrieve Not Working

Ensure you're using execute_with_auto_retrieve (not execute_command)
Check if command output file exists: ls /tmp/claude_output_*.json
For long commands, use execute_with_streaming instead

Database Issues

If commands execute but aren't saved to the database:

Check database integrity:

sqlite3 ~/.claude-command-runner/claude_commands.db "PRAGMA integrity_check;"

If corrupted, backup and remove:

mv ~/.claude-command-runner/claude_commands.db ~/.claude-command-runner/claude_commands.db.backup
# Restart Claude Desktop - a new database will be created automatically

Architecture

  ┌──────────────────┐                     ┌──────────────────┐
  │  Claude Desktop  │                     │   Warp Agent     │
  │   (TS client)    │                     │  (rmcp client)   │
  └────────┬─────────┘                     └────────┬─────────┘
           │ stdio                                  │ stdio
           │ MCP                                    │ MCP
           └──────────────────┬─────────────────────┘
                              ▼
              ┌─────────────────────────────────┐
              │   claude-command-runner v6.0    │
              │      (Swift, MCP server)        │
              │      • 39 tools                 │
              └─────────┬─────────┬─────────────┘
                        │         │
              ┌─────────┘         └──────────────┐
              ▼                                  ▼
   ┌────────────────────┐          ┌─────────────────────────┐
   │   Warp Terminal    │          │   Optional shell shim   │
   │  warp:// deeplinks │◀────────▶│ /tmp/ccr-shell-shim-    │
   │  OSC 777 events    │          │   <uid>.sock (NIO)      │
   │  AppleScript (typ) │          │   preexec/finished      │
   └────────────────────┘          └─────────────────────────┘
                        │
                        ▼
               ┌─────────────────┐
               │   Remote Hosts  │
               │    (via SSH)    │
               └─────────────────┘

Two MCP consumers, one server. Tab/window operations use Warp's warp:// URL scheme; status events use OSC 777 (printf-built); typing into a specific tab still uses AppleScript keystrokes (no Warp API exists for that). Optional shell shim adds clean preexec / command_finished events over a per-uid Unix socket.

Contributing

We love contributions! Here's how:

Fork the repository
Create a feature branch (git checkout -b feature/amazing-feature)
Commit your changes (git commit -m 'Add amazing feature')
Push to the branch (git push origin feature/amazing-feature)
Open a Pull Request

Development Setup

git clone https://github.com/yourusername/claude-command-runner.git
cd claude-command-runner
swift package resolve
swift build

💖 Support This Project

If Claude Command Runner has helped enhance your development workflow or saved you time with intelligent command execution, consider supporting its development:

Your support helps me:

Maintain and improve Claude Command Runner with new features
Keep the project open-source and free for everyone
Dedicate more time to addressing user requests and bug fixes
Explore new terminal integrations and command intelligence

Thank you for considering supporting my work! 🙏

License

MIT License – see LICENSE file for details

Built with ❤️ by 🍍

If you find this project helpful, give it a ⭐ and try Warp Terminal!