How do I add folders to spotlight search priority?
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 &lt;&lt;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