[WIP] Refactor developer_manual/conf.py to v2 user_manual style

[Copilot]

• Analyze current developer_manual/conf.py and user_manual/conf.py structures
• Update header comments to follow modern, clean style from user_manual
• Clean up import statements (import os, sys instead of import sys, os)
• Remove legacy commented-out default values that add no documentation value
• Group configuration blocks logically with proper section headers and Sphinx doc links
• Replace deprecated master_doc with modern root_doc
• Fix LaTeX preamble escape sequence warning
• Improve formatting consistency (spacing, alignment)
• Ensure all functional configurations are preserved
• Test that refactored configuration builds successfully
• Verify no functionality is lost in the refactoring

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