When creating or modifying Markdown (.md) files, Apply function only partially creates/updates file

[glerner]

Issue: When creating or modifying Markdown (.md) files, the Apply function only partially creates/updates the file

Reproduction Steps:
Create or modify a .md file in chat
Click Apply
Check the resulting file - only part of the content is saved
Example: CONTRIBUTING.md file only contains the first few sections when applied, despite the full content being provided in the chat
Workaround needed: Manual creation/editing of .md files instead of using Apply
Additional note: This seems specific to .md files, as code files (.php, .css, etc.) appear to work correctly with Apply