CLIS - AI-Powered Terminal Assistant

Claude Code Skills Alternative for DeepSeek/Qwen/Ollama

Quick Start • Usage • Commands • Documentation

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🎯 What is CLIS?

CLIS (Command Line Intelligence System) brings Claude Code's intelligent tool calling capabilities to open-source LLMs with advanced self-healing architecture:

• ✅ Self-Healing PEVL Architecture - Plan-Execute-Verify Loop with auto-replanning ⭐ NEW
• ✅ Hybrid Model Strategy - R1 planning + Chat execution (62% cost savings vs pure R1)
• ✅ Intelligent Mode Selection - R1 auto-selects optimal mode (no manual --mode needed) ⭐ NEW
• ✅ 96% cost savings - < $0.003/query (DeepSeek) vs $20/month (Claude Code)
• ✅ 42 tools - Complete editing, search, analysis capabilities
• ✅ Intelligent Memory - AI automatically references historical task experience
• ✅ Open Skills System - Customizable domain knowledge (vs Claude's closed skills)
• ✅ Offline mode - Ollama support for complete privacy
• ✅ Cross-platform - Windows/macOS/Linux

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🚀 Quick Start

Installation

# Clone repository
git clone https://github.com/Geoion/clis.git
cd clis

# Install (all dependencies will be installed automatically)
pip install -e .

Initialize

# Interactive setup
clis init

# Or specify provider
clis init --provider deepseek  # Low cost (recommended)
clis init --provider ollama     # Free, offline
clis init --provider qwen       # Chinese-optimized

First Command

# Auto mode (default) - R1 selects optimal strategy
clis run "create Flask web service"
clis run "list all Python files"
clis run "show my git changes"

# Manual mode selection
clis run "simple task" --mode=fast     # Quick execution
clis run "complex task" --mode=auto    # PEVL with self-healing

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💡 Usage

Git Workflow (Complete)

clis run "show git status"
clis run "show my changes"
clis run "commit modified files by directory"
clis run "push to remote"
clis run "create a new feature branch"
clis run "pull latest changes from main"

Docker Management

clis run "list running containers"
clis run "show logs of web-app"
clis run "restart web container"
clis run "show container stats"

Code Editing & Analysis

clis run "find all TODOs in Python files"
clis run "replace print with logger in main.py"
clis run "check linter errors in src/"
clis run "show me functions matching pattern 'async def.*'"

System & Background Tasks

clis run "show system info"
clis run "is port 8000 open?"
clis run "show top CPU processes"
clis run "start dev server in background"
clis run "list background processes"

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🧠 Intelligent Memory System (New Feature)

Automatic Historical Learning ⭐

AI automatically references similar historical task experience:

# First time doing something
clis run "configure Docker container"
# → AI learns from scratch

# Second time doing something similar
clis run "deploy Docker service"
# → 💡 AI automatically finds previous Docker tasks
# → 💡 Automatically references historical experience and solutions
# → Faster and more accurate!

Manual History Search

# Search for similar tasks
clis memory similar "Docker configuration"

# View details
clis memory show <task_id>

# View subtasks
clis memory subtasks <task_id>

# Manage memory
clis memory list
clis memory stats
clis memory cleanup

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📋 Commands

Core Commands

# Run query (tool calling enabled by default)
clis run "your query"

# Disable tool calling
clis run "your query" --no-tool-calling

# Create custom skill
clis skill create "skill-name"
clis skill create "description" --auto  # AI-generated

# List all skills
clis skill list

# View configuration
clis config show

# Check health
clis doctor

# Debug mode
clis --verbose run "your query"

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🛠️ Available Tools (40)

Filesystem (20)

Basic Operations (6):

• list_files, read_file, write_file, delete_file, get_file_info, file_tree

Search Functions (3):

• search_files - File content search
• grep - Enhanced search (regex) ⭐
• codebase_search - Semantic search ⭐

Code Editing (4):

• edit_file - Precise editing (diff mode) ⭐
• search_replace - Batch replacement (regex) ⭐
• insert_code - Line-level insertion ⭐
• delete_lines - Line range deletion ⭐

Code Analysis (4):

• find_definition - Find definitions ⭐
• find_references - Find references ⭐
• get_symbols - Extract symbols ⭐
• read_lints - Linter integration ⭐

Others (3):

• Various utility tools

Git (8) - Complete Workflow

• git_status - Repository status
• git_add - Stage files
• git_commit - Commit changes
• git_push - 🆕 Push to remote (with upstream support)
• git_pull - 🆕 Pull from remote (with rebase support)
• git_branch - 🆕 Branch management (list/create/delete/rename)
• git_checkout - 🆕 Switch branches or restore files
• git_diff - View changes
• git_log - Commit history

Docker (4)

• docker_ps - List containers
• docker_logs - Container logs
• docker_inspect - Container details
• docker_stats - Resource usage

System (5)

• system_info - OS, CPU, memory
• check_command - Verify command availability
• get_env - Environment variables
• list_processes - Running processes
• run_terminal_cmd - 🆕 Execute commands (with background support)

Network (2)

• http_request - HTTP requests
• check_port - Port availability

General (2)

• execute_command - Execute shell commands
• git_status - Quick git status (built-in)

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🔧 Configuration

Provider Setup

DeepSeek (Recommended for Cost)

clis init --provider deepseek
export DEEPSEEK_API_KEY="your-key"
# Cost: ~$0.003/query

Ollama (Recommended for Privacy)

# Install Ollama from https://ollama.ai
ollama pull llama3
clis init --provider ollama
# Cost: $0 (completely free)

Qwen (Chinese-Optimized)

clis init --provider qwen
export QWEN_API_KEY="your-key"

Context Window Configuration

Edit ~/.clis/config/llm.yaml:

model:
  name: deepseek-chat
  context:
    window_size: 64000      # deepseek-chat: 64K, deepseek-coder: 128K
    auto_chunk: true        # Enable automatic file chunking
    chunk_overlap: 200      # Overlap lines between chunks
    reserved_tokens: 4000   # Reserved for system prompt

🌟 Key Features

Open Skills System

Unlike Claude Code's closed skills, CLIS uses open, customizable Skills:

• 📝 Markdown format - Easy to read and edit
• 🔧 User-definable - Create skills for any domain
• 🤝 Community-driven - Share and collaborate
• 🎯 Fine-grained control - Safety rules, platform compatibility

See skills/ directory for examples (Docker, Git, etc.)

Enhanced Code Editing

• edit_file: Precise editing with diff preview and dry-run mode
• grep: Regex search with context lines
• read_lints: Automatic linter integration

Complete Git Workflow

Full git operations from status to push, including branch management

Background Process Support

Run long-running tasks (dev servers, builds) in background with process management

🛡️ Safety

Three-layer protection system ensures safe command execution:

1. Blacklist Protection - Blocks dangerous patterns

   • Destructive commands (rm -rf /, dd, mkfs)
   • System modifications without confirmation
   • Fork bombs and malicious patterns

2. Risk Scoring (0-100) - Automatic risk assessment

   • Low (0-30): Read-only operations - Auto-execute
   • Medium (31-60): Write operations - Require confirmation
   • High (61-90): Destructive operations - Require confirmation
   • Critical (91-100): System-level operations - Blocked

   Examples:

   • ls -la → 10 (low) → Auto-execute
   • git add . → 50 (medium) → Confirm
   • git push → 70 (high) → Confirm
   • git push --force → 95 (critical) → Blocked
   • rm -rf dir → 85 (high) → Confirm
   • sudo apt install → 95 (critical) → Blocked

3. User Confirmation - Interactive approval for risky operations

   • All high-risk tools require explicit approval
   • Risk score and level displayed for transparency
   • File modifications, git operations, deletions always confirmed

All tools have explicit risk scores and confirmation requirements. Configure behavior in ~/.clis/config/safety.yaml.

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🤝 Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

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📄 License

Apache License 2.0 - see LICENSE file for details.

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🔗 Links

• Homepage: https://github.com/Geoion/clis
• Issues: https://github.com/Geoion/clis/issues
• Documentation: https://github.com/Geoion/clis#readme