the details are listed here
Customisations to the Confluence email templates will need to be reapplied when you upgrade Confluence. Consider this before making drastic changes to the layout, and be sure to keep a list of what you have changed for your upgrade process later.
Only administrators with access to the server where Confluence is running can modify the Confluence email templates.
Process to change the email templates
1.Shut down your test instance of Confluence.
2.In the Confluence web application folder, find the file /confluence/WEB-INF/lib/confluence-2.x.jar.
3.Make a copy of this file as a backup.
4.Learn how to edit files within .jar archives.
5.Within the jar file, find the /templates/email folder. Find the appropriate file(s) within that folder.
6.Edit the file with a text editor to make the required changes. The content is mostly HTML, but has some Velocity template variables in it. See Velocity Template Overview for more information about how these work.
7.Again using the guide on editing files within .jar archives, either rejar the set of folders or drop the new files into the identical folder structure in the WEB-INF/classes directory.
8.Start Confluence up again and test your changes.
9.Apply the changes to your production Confluence instance.
The same process can be applied to modify most of the templates in the Confluence web application. For velocity files that are not in a jar file, you need not shut down and restart Confluence. Be careful to test your changes before applying them to a live site. The templates contain code that is vital for Confluence to function, and it is easy to accidentally make a change that prevents use of your site.
For me jar alternation and replacement did not work since there was some conflicting chars in the css, however placing the vm files under WEB-INF/classes worked fine for me after sorting out the css. e.g I replaced the header.vm and footer.vm under the folder \templates\email\html\includes with exactly the same folder hierarchy and it worked for me.