I am using 2.6.1 to build our site gallery and using LocalFiles Editor to create some modified template files.  I have created a new directory template-extension/OurTemplates to contain the files.

In the editor I use "Create new file" and start, for example, with:
File name: Our_footer.tpl
Parent directory: template-extension/OurTemplates
Model: default/footer.tpl

I edit the file and Save.  The file is saved as template-extension/Our_footer.tpl, not template-extension/OurTemplates/Our_footer.tpl as expected.

For now I am moving the new file to the correct directory but it is an extra step I'd rather not do.