feat: add annotation CLI and dependency profiles

[byemaxx]

This pull request introduces a command-line interface (CLI) for annotation workflows, adds flexible installation profiles for different use cases (lightweight CLI, Analyzer, Report, and GUI), and documents the new automation and result schema contracts. It also improves error handling for missing dependencies, exposes structured annotation metrics, and updates the documentation and example usage to reflect these enhancements.

The most important changes are:

1. New Features and CLI Integration

• Added a new annotation CLI (metax-annotate) for Qt-free, automation-friendly global and unit-specific annotation workflows, with full documentation and configuration file support. [1] [2] [3] [4]
• Introduced a machine-readable result JSON schema (2.0) for annotation runs, detailing run status, parameters, metrics, outputs, and diagnostics.

2. Installation Profiles and Dependency Management

• Added optional dependency profiles for Analyzer, Report, and GUI, with clear user guidance and error messages if required extras are missing. [1] .github/workflows/installation-profiles.yml [2] [3] [4]
• Updated README.md and README_PyPi.md to describe the new installation profiles and how to use the CLI, Analyzer, Report, and GUI stacks. [1] [2] [3] [4]

3. Backend and Workflow Enhancements

• Unified the annotation backend for both CLI and GUI, ensuring consistent results and metrics.
• Exposed annotation run statistics and output metrics as structured data for workflow automation and reporting.

4. Documentation and Example Updates

• Added a comprehensive CLI integration guide and updated cookbook examples to use the new CLI entry point and configuration options. [1] [2] [3] [4]
• Updated change log to reflect these major additions.

5. Testing and Validation

• Added GitHub Actions workflow to test all installation profiles (base, Analyzer, Report, GUI, full), ensuring that imports and CLI commands work as expected without unnecessary dependencies. (.github/workflows/installation-profiles.yml .github/workflows/installation-profiles.ymlR1-R61)

These changes make MetaX more modular, automation-ready, and user-friendly for both command-line and desktop use cases.

[byemaxx]

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[chatgpt-codex-connector]

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