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Thanks to vikraman: The agda-lib-ffi package provides some additional haskell modules which are needed by the agda standard library, such as during compilation using the MAlonzo backend. It is available inside the ffi/ directory and needs to be built and installed by the ebuild. (Portage version: 2.2.7/cvs/Linux x86_64, signed Manifest commit with key 618E971F)
Bump agda-stdlib snapshot to 20130109, install .agda and .agdai files with --preserve-timestamps (Portage version: 188.8.131.52/cvs/Linux x86_64, signed Manifest commit with key 618E971F)
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