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Okay no problem with the MANIFEST file then.
But the directory structure looks strange.
usr/share/cmake-2.6.0-CYGWIN-unknown usr/share/doc/cmake-2.6.0-CYGWIN-unknown/ usr/share/doc/cmake-2.6.0/MANIFEST
Shouldn't that be
usr/share/cmake-2.6.0 usr/share/doc/cmake-2.6.0/
If the subdirectory cmake-2.6.0-CYGWIN-unknown is ok then at least move the manifest file from usr/share/doc/cmake-2.6.0/MANIFEST to usr/share/doc/cmake-2.6.0-CYGWIN-unknown
12227 ./bin 4 ./share/doc/Cygwin 656 ./share/doc/cmake-2.4.8 660 ./share/doc 284 ./share/man/man1 284 ./share/man 89 ./share/cmake-2.4.8/Templates 214 ./share/cmake-2.4.8/Modules/Platform 1325 ./share/cmake-2.4.8/Modules 12 ./share/cmake-2.4.8/include 1426 ./share/cmake-2.4.8 2370 ./share
The MANIFEST file was here: ./share/doc/cmake-2.4.8/MANIFEST
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