tools: add DOT and JSON graph output support

[adulau]

Motivation

• Provide alternative serialized outputs (Graphviz DOT and JSON graph) for easier visualization and integration with other tooling.
• Avoid duplicating relationship generation logic by building a shared in-memory graph model before serialization.

Description

• Refactored tools/gen_graphml.py to produce a shared graph model via GraphNode and GraphEdge and a new build_graph() that returns (nodes, edges) instead of writing XML directly.
• Added GraphNode / GraphEdge dataclasses and new serializers to_dot() (Graphviz DOT) and to_json_graph() (JSON object with nodes and edges).
• Restored GraphML serialization via a new build_graphml(nodes, edges) function and added a CLI option --output-format with choices graphml, dot, and json-graph (default graphml).
• Preserved existing behavior for explicit and inferred relationships (--no-existing-relationships, --cross-cluster-matching) and updated the success message to include the selected output format.

Testing

• Ran python3 tools/gen_graphml.py --help which displayed the updated CLI options and succeeded.
• Generated GraphML with python3 tools/gen_graphml.py --output /tmp/test.graphml --output-format graphml which wrote the GraphML file successfully.
• Generated DOT with python3 tools/gen_graphml.py --output /tmp/test.dot --output-format dot --cross-cluster-matching value which wrote the DOT file successfully.
• Generated JSON graph with python3 tools/gen_graphml.py --output /tmp/test.json --output-format json-graph --no-existing-relationships and validated it with python3 -m json.tool /tmp/test.json, which succeeded.

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