axm-protocols / axm-init / 21981549774

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docs: update architecture, add --agent docs, and MCP how-to

Rewrite architecture page: CheckEngine (not Auditor), add checks/
layer (7 modules), tools/ layer (MCP), makefile adapter, all models.
Update README test count 317 → 379, add --agent flag to CLI table.
Add --agent section to howto/check.md and to reference/cli.md.
Add howto/mcp.md for InitCheckTool and InitScaffoldTool.
Update mkdocs.yml nav with MCP entry.

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