<!-- generated file with missing ids -->
<!ENTITY missing-ids SYSTEM 'C:/cygwin/home/David/phpdoc/entities/missing-ids.xml'>
I'm certainly no cygwin expert, but I think this should be either:
<!ENTITY missing-ids SYSTEM
'/home/David/phpdoc/entities/missing-ids.xml'>
OR
<!ENTITY missing-ids SYSTEM
'/cygdrive/c/cygwin/home/David/phpdoc/entities/missing-ids.xml'>
from within cygwin.
Theoretically yes, but since the jade we suggest to set up does not support cygwin path values, we suggested people to cd to the c: drive root first, and cd to the phpdoc folder from there...
David, please install the PHP package in cygwin (with the cygwin setup tool - it will not affect your normal PHP install), and try again. The file-entities script is ready to handle the PHP version installed by cygwin correctly. And it will generate the right /cygdrive path values then, which openjade will notice. I hope :)
Goba