Upload these v4.2.0 to your server:
(overwriting any of the older v4 files of the same name)

shop.php
admin.php
aom.php (delete this file - it is no longer needed)
/aom/cfg.css.php
/aom/cfg.default.php
/aom/cfg.lang.php
/aom/cfg.minicart.php
/aom/cfg.mp3clips.php
/aom/cfg.os.php
/aom/cfg.sha256.php
/aom/cfg.soap.php
/aom/cfg.wordpress.php
/aom/images/[all files]
/aom/js/[all files]
/ioncube/[all files]

Since v4.2.0, we use ionCube PHP Encoder to protect our source code. Associated files are found in the /ioncube directory. Normally, simply uploading these files to your server will be all that is required. If you have any problems related to ionCube, please more in-depth ionCube installation instructions.

Now that the upgraded files are on your server, it's time to open the
Associate-O-Matic Control Panel (e.g. http://www.yourdomain.com/admin.php)

When you open the Control Panel it will pull in all your previous settings and also give you access to any new and enhanced settings which will be marked as such.

At this point you'll want to make sure you enter your correct Amazon Associate ID, Amazon Access Key ID and Amazon Secret Access Key. Please see the Amazon section of our documentation for more information. Also, enter the main information for your store. Please see the Site section of our documentation for more information.

Go ahead and customize your store further by using any of these new settings making sure to save your new setting before exiting.

For those with mod_rewrite enabled, grab the latest set of rules here and update your .htaccess file accordingly. Remember not to overwrite any customizations you've made to your mod_rewrite rules (last updated v4.2.0)

Custom subcategories are now maintained inside the control panel. If you use the /aom/cfg.nodes.php file, your Subcategories will be pulled into the control panel automatically under the Subcategories section. Once loaded it creates a backup to /aom/cfg.nodesBACKUP.php as the original file is no longer used by AOM.

Congratulations! Your store is upgraded. View it in a browser.

Because many of the file names and directory structures have changed in v4, it is recommended that you start with a fresh installation.

Follow the Installation Instructions here as if you were installing Associate-O-matic for the first time.

Once installed, re-upload your cfg.saved.php file (saved settings) back to the /aom directory where it previously resided.

If you used custom graphics (e.g. buttons, icons, etc) in a previous version, you'll want to move all of those graphics to the new /aom/images directory.

Now that all of the files are on your server, it's time to open the Associate-O-Matic Control Panel (e.g. http://www.yourdomain.com/admin.php)

When you open the Control Panel it will pull in all your previous settings and also give you access to any new and enhanced settings which will be marked as such.

Go ahead and customize your store further by using any of these new settings making sure to save your new setting before exiting.

For those with mod_rewrite enabled, grab the latest set of rules here and update your .htaccess file accordingly. Remember not to overwrite any customizations you've made to your mod_rewrite rules. Last updated v4.2.0

If you use the cfg.nodes.php file, it is has been revamped. You'll need to reformat your existing custom subcategories to use the new format.

Congratulations! You're upgraded. View your store from within a web browser.