Code showing how easy it might be to handle symlinking a plugin in in WordPress 3.6 if trac ticket #xxxx is accepted

symlinkable-plugin-base.php

<?php
class Symlink_Fixer {
  var $plugin_file;
  var $plugin_id;
  function __construct( $args = array() ) {

    global $pagenow, $wp_plugin_file, $wp_plugin_slug;
    $this->$plugin_file = $wp_plugin_file
    $this->$plugin_id = $wp_plugin_slug;

    if ( 'plugins.php' == $pagenow ) {
      add_action( 'plugins_loaded', array( $this, 'plugins_loaded' ) );
      add_action( "activate_{$this->plugin_id}", array( $this, 'activate_plugin' ), 0 );
      register_activation_hook( $this->plugin_id, array( $this, 'activate' ) );
    } else  {
      register_deactivation_hook( $this->plugin_id, array( $this, 'deactivate' ) );
    }
    register_uninstall_hook( $this->plugin_id, array( parent::plugin_class, 'uninstall' ) );

  }

}