feat(application): add cross-layer graph workflows
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## Tool Contract Impact
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<!-- If this PR adds, removes, or modifies MCP tools, list them here. -->
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<!-- The current inventory is 80 tools (33 direct + 10 enhanced + 5 native + 2 artifact + 8 browser + 4 Electron + 18 session). Canonical facts: docs/product-catalog.json. -->
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<!-- The current inventory is 82 tools (33 direct + 10 enhanced + 5 native + 2 artifact + 8 browser + 4 Electron + 2 application + 18 session). Canonical facts: docs/product-catalog.json. -->
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## Related Issues
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