Description of the bug

This may not be the biggest issue, but I recently found that running nf-core sync causes ignored files to be deleted.
This is a particular nuisance as it deletes editor config files such as .vscode/.

Currently the delete is performed using a simple iteration over the files in the directory, skipping the .git folder.
It could be possible to leverage the git.Repo object to skip ignored/untracked files too.

Command used and terminal output

No response

System information

nf-core tools 2.7.2