I am using a distro with Nautilus. I want to be able to clean up the rt-click "open with" menu because it has misnamed links and links that do not work because the pathway is empty - if I can figure out how to do this once I am there.

I need to know how to get there first. I cannot find this location with Nautilus

This will take you there. In Nautilus enable hidden files to see it.

I would be rather cautious about deleting files in that directory. All those files and directories whose names are prefixed by . are personal configuration settings. If you delete them, you will lose the personalisation you have done on applications.

Alternately, press Ctrl-H in Nautilus to view hidden files.

You did not mention what desktop environment you are using, but you could look in the system settings routine (whatever your DE calls it) for something called "file associations, "default applications" (that's what Gnome calls it), or the like, and change the file associations there.

The tilde (the ~ symbol) means the currently logged in user's "home" directory/folder. The dot at the beginning of a file or directory name makes it a "hidden" file or directory in Linux and UNIX. Which is the reason it isn't displayed by default, and you therefore need to tell whatever graphical file manager program to display "hidden files" to actually see them.

If you use the ls command without any arguments it won't display "hidden" files or directories by default either. Even if you use the -l argument it won't display "hidden" files or directories, unless you use -la as the argument to ls. The bottom line is, you need to use the a argument to tell ls to display "hidden" files and directories.

In other systems like DOS, it's actually an "attribute" that's set on the file that makes it a "hidden" file. But Linux and UNIX use the dot at the beginning of the file or directory name to mark it as "hidden" oddly enough...

Strictly speaking there are no hidden files. Linux files don't wear invisibility cloaks like Harry Potter. There is simply a convention that if a filename begins with a dot, file managers will ignore it unless told otherwise. Graphical file managers have an eye symbol that you can toggle to make them display these files. The ls command uses -a for "all".

These files are nearly always configuration files and there are a lot of them in your home directory. If they routinely appeared in listings, it would be hard for your eyes to pick out the files that contain actual data. So they are usually "hidden" for your convenience.

Files or directories that really need to be hidden for security reasons are usually just given access permissions that prevent you from reading them.

And you could say the same for any other operating system too, it's not a concept unique to Linux or UNIX. It's still just an attribute that can be applied to files (and directories) that says "don't display this file(s) unless explicitly told to do so", otherwise there would be no point in having such an attribute in the first place. The only difference is how a file or directory is marked as "hidden", which obviously depends on the operating system you're using (once again, just because Linux and UNIX use a dot for that purpose, doesn't mean every other OS does, and I'd be willing to bet, like MS-DOS, and last time I checked, Windows uses an "attribute" set on said file(s) to mark it as "hidden"). Computers are just machines that do what they're told to do, they aren't "magical" anymore than software is. So what does Harry Potter have to do with anything here ? The "read-only" attribute isn't "magical" either, it simply just means, "this file/directory cannot be deleted while it's marked as read-only", nothing "magical" about that. Also, not all graphical file managers have an "eye symbol", it depends on the file manager you're using as to how to get it to display files marked as "hidden".

In any case, I think we've already well covered the fact that Linux and UNIX use a dot at the beginning of the file or directory name to mark something as "hidden", and that you therefore need to explicitly tell a graphical file manager or ls to display such files, as was already mentioned above beforehand anyway. So not sure why it needs to be restated again...

I think you already covered that in post #3, so not sure why it needs to be restated again.

That assumes you're talking about an operating system that actually supports permissions. In MS-DOS for one example, which does not support any file permissions of any kind, IO.SYS and MSDOS.SYS were "hidden" to protect them from deletion. Because if either one of them was deleted, you would break MS-DOS and it would not boot at all. IO.SYS contained basic drivers, while MSDOS.SYS contained the MS-DOS kernel. Although COMMAND.COM, and while essential as well, wasn't actually "hidden", but since it was the DOS shell, it's what displayed the "MS-DOS prompt"/command-line and contained internal commands like the cd command (which done the same thing for DOS as what it does for Windows, Linux and UNIX).

In regards to Linux, I think avoiding the user unwittingly deleting said settings (thinking you don't need said files for whatever reason(s)) or otherwise modifying them unnecessarily, and/or incorrectly, as much as they are "hidden" by default so you don't get "confused".

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Thanks ! Done.