docs: regenerate all 13 AGENTS.md files from deep codebase exploration

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YeonGyu-Kim
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## OVERVIEW
Configuration orchestration layer. Runs once at plugin init — transforms raw OpenCode config into resolved agent/tool/permission structures.
Configuration orchestration layer. Runs once at plugin init — transforms raw OpenCode config into resolved agent/tool/permission structures via 6-phase sequential loading.
## STRUCTURE
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