I decided it was most beneficial to group the files together by plugin (scenario #1 in my comment above).
I also spun off the plugin "templates" directory issue into a separate bug: https://bugs.launchpad.net/mahara/+bug/1328319
Also, I realized that /local/theme template files were *not* overriding normal theme files like I thought they were. So I spun off another bug to make that work the way I expected it to: https://bugs.launchpad.net/mahara/+bug/1328310
I decided it was most beneficial to group the files together by plugin (scenario #1 in my comment above).
I also spun off the plugin "templates" directory issue into a separate bug: https:/ /bugs.launchpad .net/mahara/ +bug/1328319
Also, I realized that /local/theme template files were *not* overriding normal theme files like I thought they were. So I spun off another bug to make that work the way I expected it to: https:/ /bugs.launchpad .net/mahara/ +bug/1328310