Why does ls -a not show files that finder does show? When navigating to /usr/local/bin a file called &quot;R&quot; can be seen:

But when cd /usr/local/bin and ls (or ls -a), we see a long list of files, but no file called R:

I was surprised by this - apparently finder can see files that ls cannot. Why doesn't ls -a show all files that finder does?
It's there, but you're not seeing it because it's not where you're expecting it to be because the sorting in Finder is different than the sorting in Bash/Zsh.  Basically Finder does a case insensitive search whereas Bash is case sensitive.  For example, &quot;a&quot; follows &quot;Z&quot;
If you're looking for a specific file and you know the case, you can use a little ls magic to find it...
$ ls -Ad R*

Where...

-A = List all files, except . and ..
-d = Treat directories as files and do not search them recursively
R* = All files that begin with the letter &quot;R&quot;