IOS – Hiding iCloud folders from search on iOS

A Finder alias (not a symlink) will be added to spotlight, if it's sitting in a visible folder, like Applications.

You can create them programmatically using AppleScript (use osascript to integrate with other shell scripts.)

To create an alias use make alias file to {file to alias} at {destination of alias}.

By default (ie. if destination isn't specified) the alias is created on the current user's Desktop, ie. ~/Desktop.

Here's an example script to create an alias of a file in /Applications

set target_app to POSIX file "/usr/path/to/app"
set alias_dest to POSIX file "/Applications"

tell application "Finder"
  make alias file to target_app at alias_dest
end tell

By the way, osascript accepts input from stdin, so to run an AppleScript in a shell script, using a heredoc will work. It may make it easier for you to setup the target file better:

#!/bin/bash
TARGET=/usr/path/to/app
osascript <<EOS

set target_app to POSIX file "$TARGET"
set alias_dest to POSIX file "/Applications"

tell application "Finder"
  make alias file to target_app at alias_dest
end tell

EOS

This ended up being a SuperDuper! problem. It was doing a fresh copy rather than a smart update and when it does that, it sets the drive to be indexed in spotlight rather than retaining your previous setting. Once I set it to smart update the problem was fixed.