Running nf-core modules update --save-diff when file was created or removed

[ErikDanielsson]

Description of the bug

nf-core modules update --save-diff promises that it can write module changes to a .diff file, and then complete the update with git apply <diff-file>. If a file was removed or created, this is written as a message in the .diff file. However, git apply can't use this information, not for removing files and in particular not for creating files since the file is not available. This will lead to bugs, since the command promises more than it can deliver. I would therefore suggest that the command fails if the update involves removing or creating files, and instead suggest that the user use either the plain update command or the --preview option

Command used and terminal output

nf-core modules update --save-diff

System information

nf-core/tools 2.5dev

[ErikDanielsson]

Closing due to merge of #1698