Why does ls -a not show files that finder does show?
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;