Enhance markdown navigation links and reference formatting

[Dawsine]

Summary

This PR improves generated Markdown navigation and reference formatting.

Changes

• add anchors and internal links for references, equations, figures, and tables
• link whole single equation references such as Eq. (46), instead of linking only the parenthesized number
• keep consecutive reference entries compact by removing blank lines between them while preserving anchors
• add a focused unit test for markdown navigation rendering

Validation

• py_compile passed for the modified source file and the new unit test
• pytest passed for tests/unittest/test_markdown_navigation.py using addopts override

Notes

This PR intentionally does not include local presentation-specific postprocessing such as image centering, image renaming, or moving figures near their first textual mention.

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