Organize documentation files: move most .md files to docs directory, keep AGENTS.md in root

[Copilot]

This PR reorganizes the repository structure by moving most markdown documentation files from the root directory to the existing docs/ directory, creating a cleaner and more organized project layout while keeping essential files accessible to AI tools.

Changes Made

Files Moved to docs/ directory:

• ADVANCED_USAGE.md → docs/ADVANCED_USAGE.md
• AI_DYNAMIC_TOOLS_FAQ.md → docs/AI_DYNAMIC_TOOLS_FAQ.md
• CONFIGURATION.md → docs/CONFIGURATION.md
• DEPLOYMENT.md → docs/DEPLOYMENT.md
• DYNAMIC_TOOLS_GUIDE.md → docs/DYNAMIC_TOOLS_GUIDE.md
• INTEGRATION.md → docs/INTEGRATION.md
• MOD_DEVELOPMENT.md → docs/MOD_DEVELOPMENT.md
• OPENAI_TOOL_NORMALIZATION.md → docs/OPENAI_TOOL_NORMALIZATION.md
• SOLUTION_SUMMARY.md → docs/SOLUTION_SUMMARY.md

Files Kept in Root Directory:

• README.md (primary entry point)
• AGENTS.md (kept at root level for codex/AI tool discovery)

Reference Updates:

• Updated all documentation links in README.md to point to the new docs/ paths
• Updated the reference to AGENTS.md in .github/copilot-instructions.md

Benefits

• Cleaner root directory: Reduces clutter in the repository root while keeping essential files accessible
• Better organization: Most documentation is now centralized in the docs/ directory alongside the existing architecture-flow.svg
• AI tool compatibility: AGENTS.md remains at root level for easy discovery by codex and other AI tools
• Maintained functionality: All links have been updated to preserve navigation
• No breaking changes: The project builds and tests continue to pass without issues

The README.md and AGENTS.md files remain in the root directory as primary entry points, while all other supporting documentation is properly organized in the dedicated documentation directory.

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[pardeike]

@copilot Put the AGENTS.md file back, I think it should be top level so codex can find it there

[Copilot]

@copilot Put the AGENTS.md file back, I think it should be top level so codex can find it there

Done! Moved AGENTS.md back to the root directory so codex can find it there. Also updated the reference in .github/copilot-instructions.md to point to the root location. (commit 1597efd)