Option 1: use TextMate 1:
open ~/Library/Application\ Support/Avian/Bundles/Themes.tmbundle/Themes/Custom.tmTheme -a TextMate
cp ~/Library/Application\ Support/TextMate/Themes/Custom.tmTheme \
~/Library/Application\ Support/Avian/Bundles/Themes.tmbundle/Themes/Custom.tmTheme
Option 2: edit the theme as an old-style plist from the bundle editor:

Option 3: edit the tmTheme file directly by opening it with mate
:
mate ~/Library/Application\ Support/Avian/Bundles/Themes.tmbundle/Themes/Custom.tmTheme
The last two options require you to close and reopen files to make them use the edited theme. tell app "TextMate 2" to reload bundles
does not work.
You can use pl
and plutil
to convert between the XML and old style formats:
pl -input file.plist -output file.plist
plutil -convert xml1 file.plist