Though most modifications can be done on the per-package basis, some do not fit well into the packaging scheme. Notably adding add-on scripts for the dedicated feature set, such as setup, install, update, backup, ... specific for the actual appliance product. Often even defining the actual product.

T2 allows to inject additional files into the systems root filesystems (rootfs) for some output images being created, such as an LiveCD. The to be injected files just have to placed in a sub-directory named 'rootfs' inside the target directory: target/$targetname/rootfs. The whole directory tree will be copied into the final output images.

As some tweaks for the final target are modifications to existing files, or files to be removed (for example due to space constraints) special header codes are recognized to support patching, removing files or changing the permission bits. These codes mimic the classic Unix shebang ('#!') of scripts, just that no absolute path follows the marker ('#!') in these T2 overlay codes, but the action to perform, such as: '#!patch', ''#!chmod', '#!chown', '#!rm', #!ln', and '#!cp'.