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docs: update documentation to align with v0.2.5 features and architecture
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| document/01_system_overview.md |
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| document/02_architecture_design.md |
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| document/03_database_specification.md |
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| document/04_mcp_api_specification.md |
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| document/05_sidecar_integration.md |
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| document/06_development_guide.md |
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