With that branch I get

make[3]: Entering directory `/home/martin/upstream/libindicate/libindicate'
make[3]: *** No rule to make target `Indicate-0.2.typelib', needed by `all-am'. 
 Stop.
make[3]: Leaving directory `/home/martin/upstream/libindicate/libindicate'

I can't quite see what's wrong here, though. It does work with your patch in 
the Ubuntu package.
-- 
https://code.launchpad.net/~ken-vandine/libindicate/annotation_fixes/+merge/43575
Your team ayatana-commits is subscribed to branch lp:libindicate.

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