Here's what I think those files are:
I think spotlight crashed and for some reason stored some (recovery?) info in this file.
I know of two tools that expoolicitly reference a file name "manual.auto". One is OSS 3D, for iTunes (now discontinued). The other is Hear (a more general audio enhancer). Do you or did you use either of these?
Have no idea.
You can safely remove all three.
I think you're right about manual.auto. I believe I did demo that software at some point. I admit I'm most curious about Save/ because of its peculiar name. You typically can't use a slash in a filename since that indicates a directory. It's also curious that it consists of zero KB. For what purpose would an app create a filename with a slash?
Actually, in the finder, you can create a filename which looks like it has a slash in it. That's because the finder changes those explicit slashes to colons (':'). And that is why you cannot create a filename in the finder containing a colon. Try it.
In your initial post your ls of the actual file showed it was named "Save:". Note the colon. That's why it looks like "Save/" when you videw it in the finder.
The thing is empty. Don't worry about it. Just trash it.
You're right, you can save a file with a slash in it. It seems I tried that in the past, and the Finder changed them to hyphens, but I never tried it except shortly after switching from OS 9 to X.
Hope I didn't give the impression that I was "worried" about these files. I'm just a curious person. In both senses, I guess. ; )
Interestingly, I just noticed another file in my Home directory named #manual.auto# with a creation date of yesterday! That one couldn't be from Hear. It also just contains code.
There is also a manual.auto file in there that I hadn't noticed before, with a creation date that matches the one in my Root directory, (I do most of my navigating via LaunchBar).