M2MStudio is using just LF at the ends of lines; this is incorrect for native windows files - it should be CRLF.
This means, for example, that text files can’t be viewed properly in Notepad.
There’s an option in the Project Properties to change this for new files - but how can I get it changed on existing files?
Easy: open the file in the editor, and File > Convert line delimiters to > make your choice… 
So it is! 
But it does raise another question:
When I go there, the option at the top of the list is ‘Windows [default]’ - so, if Windows is the default, why is it not using Windows line-endings enyhow…? 
The project option for new files is currently ‘Inherited from container’ - so what is the “container” here? And, again, why is it not defaulting to the correct value for the current host system?
I guess that Windows is the default for new files.
M2M Studio is not going to modify all existing files in order to convert them to Windows line endings 
By the way, haven’t you a more advanced text editor than Notepad ? 
It should be the workspace: configured in Preferences > General > Workspace