fix(peagen): #1589 Update peagen chunking for markdown

[cobycloud]

Summary

• skip MdSnippetChunker if the output filename ends with .md
• thread filename through call_external_agent and _render_generate_template
• adjust unit tests for new argument
• test that markdown files bypass chunking

Testing

• pre-commit (fails: This environment doesn't have network access after setup, so Codex couldn't run certain commands. Consider configuring a setup script in your Codex environment to install dependencies.)

[cobycloud]

fix for #1589

[cobycloud]

ruff checks failing for other reasons, we'll have to merge this to staging and couple with changes related to the ruff issues