Add support for native IR input format

[melonattacker]

This pull request introduces support for native Graph IR JSON as an explicit input format for Threat Thinker, enabling users to bypass diagram parsing and directly provide a structured architecture model. The changes update CLI options, documentation, and internal input handling to integrate this new format alongside existing diagram types.

Native IR support and input handling:

• Added a new --ir CLI flag and input format for native Graph IR JSON, allowing users to supply explicit architecture models without diagram syntax. Updates include parsing logic, CLI argument handling, and error messages for unsupported formats. (src/threat_thinker/main.py, src/threat_thinker/input_loader.py, [1] [2] [3] [4] [5]
• Updated input detection and loading to centralize format dispatch, including native IR, and removed redundant parsing logic from main.py. (src/threat_thinker/main.py, src/threat_thinker/input_loader.py, [1] [2]

Documentation and example updates:

• Added a comprehensive Native IR Guide explaining the JSON schema, usage scenarios, CLI/API/Web UI integration, validation rules, and example files. (docs/ir.md, docs/ir.mdR1-R239)
• Updated CLI documentation and quick links to reflect the new --ir flag and native IR input, clarifying autodetection rules and supported formats. (docs/cli.md, docs/README.md, [1] [2] [3]
• Expanded README and design docs to include native IR as a supported input format, and clarified processing flow diagrams. (README.md, docs/design.md, [1] [2] [3] [4]

Examples and API changes:

• Added a minimal example file for native IR input, demonstrating node, edge, and zone structure. (examples/diagrams/ir/system.ir.json, examples/diagrams/ir/system.ir.jsonR1-R55)
• Updated demo proxy app to recognize the new ir input type for API requests. (examples/demo-app/proxy/main.py, examples/demo-app/proxy/main.pyR49)