Add initial Context-Engine CLI implementation

.indexignore

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+cosqa*.json
+# dev-workspace contains uploaded client workspaces - they get indexed
+# separately via upload service, not as part of the main Context-Engine repo
+dev-workspace/

pyproject.toml

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+[build-system]
+requires = ["setuptools>=45", "wheel", "setuptools_scm>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "context-engine"
+version = "0.1.0"
+description = "Context-Engine: Semantic code search and memory system with MCP tools"
+readme = "README.md"
+authors = [
+    {name = "Context-Engine Team", email = "mirlok89@gmail.com"}
+]
+license = {text = "Business Source License 1.1"}
+requires-python = ">=3.10"
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+
+dependencies = [
+    "qdrant-client>=1.15.0,<1.16.0",
+    "fastembed",
+    "watchdog",
+    "onnxruntime",
+    "tokenizers",
+    "orjson",
+    "tree_sitter>=0.25.0",
+    "tree_sitter_python>=0.23.0",
+    "tree_sitter_javascript>=0.23.0",
+    "tree_sitter_typescript>=0.23.0",
+    "tree_sitter_go>=0.23.0",
+    "tree_sitter_rust>=0.23.0",
+    "tree_sitter_java>=0.23.0",
+    "tree_sitter_c>=0.23.0",
+    "tree_sitter_cpp>=0.23.0",
+    "tree_sitter_ruby>=0.23.0",
+    "tree_sitter_c_sharp>=0.23.0",
+    "tree_sitter_bash>=0.23.0",
+    "tree_sitter_json>=0.24.0",
+    "tree_sitter_yaml>=0.7.0",
+    "tree_sitter_html>=0.23.0",
+    "tree_sitter_css>=0.23.0",
+    "tree_sitter_markdown>=0.5.0",
+    "mcp==1.17.0",
+    "fastmcp==2.12.4",
+    "fastapi",
+    "uvicorn[standard]",
+    "python-multipart",
+    "jinja2",
+    "openai>=2.11.0",
+    "openlit>=1.0.0",
+    "python-toon>=0.1.3",
+    "rich>=13.0.0",
+    "typer>=0.9.0",
+    "requests>=2.28.0",
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest",
+    "pytest-asyncio",
+    "anyio",
+    "testcontainers",
+]
+
+[project.scripts]
+ctx = "scripts.ctx_cli:main"
+ctx-cli = "scripts.ctx_cli:main"
+
+[project.urls]
+Homepage = "https://github.com/m1rl0k/context-engine"
+Documentation = "https://github.com/m1rl0k/context-engine/tree/main/docs"
+Repository = "https://github.com/m1rl0k/context-engine"
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["scripts", "scripts.*"]
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.package-data]
+"scripts.ctx_cli" = ["*.py", "completions/*.sh", "completions/*.zsh", "completions/*.fish"]

scripts/ctx_cli/README.md

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+# ctx CLI
+
+Unified command-line interface for Context-Engine.
+
+## Installation
+
+```bash
+pip install -e .
+```
+
+## Quick Start
+
+Get up and running with a single command:
+
+```bash
+ctx quickstart
+```
+
+This will:
+1. Configure your environment
+2. Start all services
+3. Index your codebase
+4. Warm up embedding models
+
+## Commands
+
+### Getting Started
+
+| Command | Description |
+|---------|-------------|
+| `ctx quickstart` | One command to rule them all - full setup |
+| `ctx init [--full]` | Interactive setup wizard |
+| `ctx doctor` | Diagnose issues with actionable fixes |
+
+### Service Management
+
+| Command | Description |
+|---------|-------------|
+| `ctx up [--build] [--wait N]` | Start services |
+| `ctx down [--volumes]` | Stop services |
+| `ctx restart [--build]` | Restart services |
+| `ctx status [--json] [--verbose]` | Show stack health, model state, cache stats |
+| `ctx logs [SERVICE] [-f] [--tail N]` | View service logs |
+| `ctx warmup [--status]` | Preload models for fast queries |
+
+### Search & Retrieval
+
+| Command | Description |
+|---------|-------------|
+| `ctx search <query> [options]` | Semantic code search |
+| `ctx answer <query> [options]` | LLM-generated answers with citations |
+| `ctx memory store <info> [--tags]` | Store knowledge in memory |
+| `ctx memory find <query> [--kind]` | Search stored memories |
+| `ctx graph callers <symbol>` | Find who calls a symbol |
+| `ctx graph definition <symbol>` | Find where symbol is defined |
+| `ctx graph importers <symbol>` | Find what imports a module |
+| `ctx graph callees <symbol>` | Find what a symbol calls |
+| `ctx pattern <query> [--mode]` | Find structurally similar code |
+
+### Indexing
+
+| Command | Description |
+|---------|-------------|
+| `ctx index [path] [--watch]` | Index codebase (local/mounted) |
+| `ctx sync [path] [--watch]` | Upload/sync to remote server |
+| `ctx prune [--collection]` | Remove stale entries |
+| `ctx collections list` | List all collections |
+| `ctx collections create NAME` | Create new collection |
+| `ctx collections delete NAME` | Delete collection |
+
+### Remote Sync (VS Code Extension Equivalent)
+
+| Command | Description |
+|---------|-------------|
+| `ctx sync` | Force sync current directory |
+| `ctx sync --watch` | Watch mode with auto-sync |
+| `ctx sync --git-history` | Include git commit metadata |
+| `ctx sync --endpoint URL` | Use custom upload endpoint |
+
+### IDE Integration
+
+| Command | Description |
+|---------|-------------|
+| `ctx bridge generate claude` | Generate Claude Desktop config |
+| `ctx bridge generate cursor` | Generate Cursor IDE config |
+| `ctx bridge generate windsurf` | Generate Windsurf config |
+| `ctx bridge generate all` | Generate all IDE configs |
+
+### Configuration
+
+| Command | Description |
+|---------|-------------|
+| `ctx config [--get K] [--set K=V]` | View/edit configuration |
+| `ctx completion [bash\|zsh\|fish]` | Shell completions |
+
+## Examples
+
+```bash
+# Quick start for new users
+ctx quickstart
+
+# Check system health
+ctx doctor
+
+# Start services and monitor logs
+ctx up --build
+ctx logs indexer -f
+
+# Search the codebase
+ctx search "database connection" --language python --snippet
+ctx answer "how does the indexing pipeline work?"
+
+# Memory operations
+ctx memory store "JWT tokens are used for auth" --kind explanation --tags topic=auth
+ctx memory find "authentication" --limit 5
+
+# Symbol graph navigation
+ctx graph callers authenticate --depth 2
+ctx graph definition MCPClient --language python
+ctx graph importers qdrant_client
+
+# Pattern search
+ctx pattern "try: ... except: pass" --snippet
+ctx pattern "retry with backoff" --mode description
+
+# Manage collections
+ctx collections list
+ctx collections create my-project
+ctx collections switch my-project
+
+# Generate IDE configs
+ctx bridge generate all
+
+# Monitor and maintain
+ctx status --verbose
+ctx warmup --status
+ctx index --watch
+```
+
+## Shell Completion
+
+```bash
+eval "$(ctx completion bash)"   # Bash
+eval "$(ctx completion zsh)"    # Zsh
+ctx completion fish | source    # Fish
+```
+
+## Configuration
+
+Config loaded from `./.ctxrc` or `~/.ctxrc`:
+
+```ini
+[indexer]
+url = http://localhost:8003
+timeout = 30
+
+[memory]
+url = http://localhost:8002
+
+[search]
+default_limit = 10
+default_collection = codebase
+
+[docker]
+compose_file = compose.yaml
+```
+
+## Environment Variables
+
+| Variable | Description | Default |
+|----------|-------------|---------|
+| `MCP_INDEXER_URL` | Indexer HTTP endpoint | `http://localhost:8003/mcp` |
+| `MCP_MEMORY_URL` | Memory HTTP endpoint | `http://localhost:8002/mcp` |
+| `COLLECTION_NAME` | Default collection | `codebase` |
+| `COMPOSE_FILE` | Docker compose file | `compose.yaml` |
+
+## Troubleshooting
+
+Run the doctor command to diagnose issues:
+
+```bash
+ctx doctor
+```
+
+Common fixes:
+- **Services not running**: `ctx up`
+- **Models not loaded**: `ctx warmup`
+- **Stale index**: `ctx prune && ctx index`
+- **Config issues**: `ctx init --env-only`

scripts/ctx_cli/__init__.py

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+#!/usr/bin/env python3
+# Copyright 2025 John Donalson and Context-Engine Contributors.
+# Licensed under the Business Source License 1.1.
+"""
+Context-Engine CLI - Unified command-line interface for MCP tools.
+
+This package provides a production-ready CLI for interacting with the
+Context-Engine MCP servers (Memory and Indexer).
+"""
+
+__version__ = "0.1.0"
+__author__ = "Context-Engine Team"
+
+try:
+    from scripts.ctx_cli.main import main
+except ImportError:
+    # Allow import to succeed even if dependencies aren't installed
+    def main():
+        """Placeholder main function when dependencies are missing."""
+        print("Error: ctx_cli dependencies not installed. Run: pip install -e .")
+        return 1
+
+# For backward compatibility
+app = main
+
+__all__ = ["main", "app", "__version__"]

scripts/ctx_cli/__main__.py

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+"""
+Entry point for running the CLI as a module.
+
+Usage:
+    python -m scripts.ctx_cli
+    python -m scripts.ctx_cli --help
+    python -m scripts.ctx_cli status
+"""
+
+import sys
+from scripts.ctx_cli.main import main
+
+if __name__ == "__main__":
+    sys.exit(main())

scripts/ctx_cli/commands/__init__.py

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+#!/usr/bin/env python3
+# Copyright 2025 John Donalson and Context-Engine Contributors.
+# Licensed under the Business Source License 1.1.
+"""
+Context-Engine CLI commands package.
+
+Available commands:
+  - quickstart: One command setup - init, start, index, and warmup
+  - up: Start services
+  - down: Stop services
+  - restart: Restart services
+  - status: Show stack status
+  - doctor: Comprehensive health check
+  - logs: View service logs
+  - init: Interactive setup wizard
+  - search: Search the codebase
+  - answer: Get natural language answer with citations
+  - memory: Store and search knowledge entries
+  - graph: Navigate symbol relationships (callers, definitions, imports)
+  - pattern: Find structurally similar code patterns
+  - index: Index codebase into Qdrant
+  - sync: Upload/sync workspace to remote Context-Engine
+  - prune: Remove stale entries from index
+  - collections: Manage Qdrant collections
+  - bridge: Manage MCP bridge and generate IDE configs
+  - warmup: Preload models to reduce first-query latency
+  - completion: Shell completion scripts
+"""
+
+from . import status, init, answer, index, prune, completion, lifecycle, search, config, logs, warmup, collections, bridge, quickstart, doctor, memory, graph, pattern, sync
+
+# List of all command modules
+COMMANDS = [
+    quickstart,  # The ONE COMMAND to rule them all
+    lifecycle,  # up, down, restart commands
+    status,
+    doctor,
+    logs,
+    init,
+    search,
+    answer,
+    memory,      # Memory store/find
+    graph,       # Symbol graph navigation
+    pattern,     # Pattern search
+    index,
+    sync,        # Remote upload/sync (like VS Code extension)
+    prune,
+    collections,
+    warmup,
+    config,
+    bridge,
+    completion,
+]
+
+
+def register_all_commands(subparsers):
+    """Register all available commands with the argument parser."""
+    for command in COMMANDS:
+        command.register_command(subparsers)