Well the file looks exactly like it should. The file is a part of the site definition. A site definition is the framework that a site is based on. It defines what a site will look like and consist of, for every site that uses that site definition. It defines things like the header going across the top of the page, and that the site will have Document Library, Events and links available for web part creation. After you create a site, all of the content you create is stored in the content database and will not appear in the site definition file. There is only one copy of AllItems.aspx on your server, regardless of how many sites you actually have created. I hope this is making sense, there is a lot of documentation out there about site definitions (you can start here: heathersolomon.com/.../resources.aspx#03TDT).
You can certainly modify your site to open links in a new window, and the 4 links I sent have 4 different ways to do it. It all depends on whether or not you want to alter the behavior for ALL links lists, or just one links list on one site.
This one creates a new list definition (similar to a site definition, defines a list and the actual content is store in the database) so you can have a links web part that allows for opening links in a new window:
andrewconnell.com/.../...sListOpenInNewWindow.aspx
These effect a single site:
mindsharpblogs.com/.../654.aspx
www.sharepointblogs.com/.../5027.aspx
wss.collutions.com/Lists/FAQ/DispForm.aspx?ID=254