I came across an issue where files being specified more than once result in the same file being included multiple times in the nupkg archive. The behaviour can be reproduced using this commit. For instance, In FsPickler.fsproj, the paket template contains the following declarations:

type project
id FsPickler
...
files
    ../../bin/FsPickler.dll ==> lib/net45
    ../../bin/FsPickler.pdb ==> lib/net45
    ../../bin/FsPickler.xml ==> lib/net45
    ../../bin/net40/FsPickler.dll ==> lib/net40
    ../../bin/net40/FsPickler.pdb ==> lib/net40
    ../../bin/net40/FsPickler.xml ==> lib/net40

This will cause the net45 FsPickler.dll to be bundled twice, but not the same for net40.

The obvious fix here would be to omit the net45 declarations, but I would prefer the explicitness of the current version.

Taking this issue to the extreme, it is possible to do the following:

files
    ../../bin/FsPickler.dll ==> lib/net45
    ../../bin/FsPickler.dll ==> lib/net45
    ../../bin/FsPickler.dll ==> lib/net45
    ../../bin/FsPickler.dll ==> lib/net45
    ../../bin/FsPickler.dll ==> lib/net45

which yields the following result: