No externals -- Embedded libraries are called "externals" because they are pulled from outside the addon's own files on the wowace.com SVN to create the .zip file. If you download with "no externals" it means you are downloading without embedded libraries; you can use the "automatic dependency download" option to assist you with managing standalone libraries. However, if you don't already know about embedded vs standalone libraries and why you might want to use either, I would recommend leaving the "no externals" setting off and just using the default embedded libraries.
Cleanup addon folders -- This means that JWU will delete files in the addon folder before writing the new files, to keep old files (such as changelogs) from piling up. After all updates are downloaded, JWU will then look through each addon's .toc file and comment out references to any files that don't exist. This is done because when WoW loads, every .toc reference to a nonexistent file slows down the loading process significantly. I would recommend leaving this option on.
Split addons... -- This means that addons like BigWigs, PitBull, and Quartz will be split up into separate addons for each module. For BigWigs this actually does have some use, as it means that the boss modules for, say, Black Temple, won't be loaded into memory until you actually zone into Black Temple. For PitBull and Quartz and most other addons that use this feature, this doesn't really serve any purpose, as the modules are loaded anyway (for example, PitBull's health bar module is always needed, so there is no reason to split it off into a separate addon). I would recommend leaving this option off as it doesn't accomplish much in most cases, and creates more clutter in your addons folder.
Phanx - thank you for the great info! I think that I got it to work correctly for me last night. A few other questions though regarding the options:
- Backup and clean variables - I did this the first time thinking that I could backup everything first and maybe it did but what does the "clean variables" mean? (Like I posted earlier when I loaded Wow after clicking this and the "Update Addons" alot of the addons were gone and/or not loading.)