Add structure dependency graph command

[httpdss]

Motivation

• Provide a way to visualize dependency relationships declared via folders[].struct / folders[].structkit so users can inspect nested structure references, detect missing targets, and find cycles.
• Expose the feature both from the CLI and as an MCP tool so it can be used interactively and programmatically (e.g., from AI-assisted clients).

Description

• Add a new CLI command GraphCommand in structkit/commands/graph.py that builds a dependency graph from structure definitions, de-duplicates edges, reports missing references and cycles, and emits text, json, or mermaid output.
• Register graph in the main CLI (structkit/main.py) and document the command in docs/cli-reference.md.
• Integrate graph functionality into MCP via _graph_structure_logic, a graph_structure tool registration, and a compatibility handler _handle_graph_structure in structkit/mcp_server.py, and document the MCP tool in docs/mcp-integration.md.
• Add tests in tests/test_graph_command.py covering single/multiple/nested dependencies, missing nodes, cycles, local YAML input, --all mode, JSON/Mermaid output, and MCP compatibility.

Testing

• Ran unit tests for the graph feature with pytest tests/test_graph_command.py -q, which passed.
• Ran the graph + MCP integration tests with pytest tests/test_graph_command.py tests/test_mcp_integration.py -q, which passed.
• Ran the full test suite with pytest -q, which passed (all tests green).

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Codex Task