I have now updated the module to include full support for the multi-site manager. It now works on a per-site basis and will export all of the templates for whichever is the ‘active’ site. So if you have two sites and wish to export both sets of templates you would first select Site A from the Sites drop-down and run T2F. Then you would select Site B from the drop-down menu and run T2F a second time. The site-specific template directory settings are respected, so the module behaviour mirrors that of EE but on a bulk basis.
The link in the first post has been updated.
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