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Refactor: Transition to Pandoc Filters #5

@Pascal-Kueng

Description

@Pascal-Kueng

The current logic relies heavily on regex to manipulate Markdown text.

Problem:
Regex is brittle against complex Markdown (escaped characters, nested spans, etc.).

Solution:
Implement a native Pandoc Lua filter (or a Python filter via panflute) to handle comment spans and milestone markers directly in the AST.

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