A working example of a TAF template is the Smartdots report. Here, there is a public repository holding the template scripts, and a private repository holding the same code, but with branches for each run of the template.
The server clones the tempate repo, and changes the remote push url to the private repository. This way changes in the public template are pulled down to the server, merged over into the individual applications of the template, and pushed back to the relavent branch.