Fix codebase.checkout() wiping out .gitignore'd files

[devin-ai-integration]

This PR fixes an issue where codebase.checkout() was wiping out .gitignore'd files like node_modules and the .codegen folder. The fix uses git stash/pop to preserve these files during checkout instead of using discard_changes() which removes them.

Reproduction steps:

• Parse a codebase with Codebase('./')
• Make some changes/do a codemod
• Call codebase.commit()
• Make some changes manually in the file (not via a codemod)
• Call codebase.checkout(commit="...")

Link to Devin run: https://app.devin.ai/sessions/f1f4c35acc5e4d9799e996c613b691a6
Requested by: [email protected]

[devin-ai-integration]

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