Committed and pushed the fix to: 
https://code.launchpad.net/~nadiana/phatch/transparency-fix
I ran the test suite after and before the changes and compared the results 
using the script. There are few visual changes. The changes are because P mode 
is now handled explicitly in 2 new cases (pdf and xbm). Before they were left 
to PIL to handle them poorly. The transparency fix didn't affect the visual 
result in the test case images, it just removed the extra transparency index.

** Changed in: phatch
       Status: Confirmed => Fix Committed

-- 
GIF transparency index is always added
https://bugs.launchpad.net/bugs/437376
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Status in Phatch = Photo & Batch!: Fix Committed

Bug description:
When an image is saved as GIF the transparency index is always written as 255 
even if there is no transparency. In many images there might be not visible 
difference. But it is possible for parts of the image to become hidden because 
of this.

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