Fix markdown parsing breaking documents into tiny sections

## Problem
The tool incorrectly parses markdown files by breaking them into tiny sections for each header and list item, which destroys the document structure.

## Expected Behavior
Markdown files should be treated as a single content section to preserve their structure and formatting.

## Actual Behavior
Every header (h1-h6) and list item is parsed as a separate section, breaking the document flow.

## Steps to Reproduce
1. Create a markdown file with multiple headers and lists
2. Parse it with the tool
3. Observe that each element becomes a separate section

## Impact
This makes the tool unusable for merging markdown documentation files as it completely destroys the document structure.

Start by locating the Go entry point that parses Markdown files and reproduce the issue with a document containing multiple headers and lists. Done means a Markdown file is treated as one content section, preserving its document flow and formatting during merging.

Written by the indexing model from the issue text.