The MANIFEST files just lists the names of the files that need to be included in a Perl distribution. When packaging the distribution Perl will use this list to determine what to include. When unpacking the tarball Perl will check if the files that were unpacked are the exact same files that are listed in the MANIFEST file. No other file is included and no file is missing.

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Some people maintain the MAINFEST file manually and keep in it version control.

Others keep a file called MANIFEST.SKIP that basically contains regular expressions describing which files should be excluded from the distribution zip file.

Then just before creating the distribution the author runs a command that will go over all the directories in the directory tree of the project listing all the files exlucing the onese matched by one of ther regular expressions in the MANIFEST.SKIP.

The files that are not filtered out are used to compose the content of the MANIFEST file.

In this case the author would keep the MANIFEST.SKIP in the version control system, but would not keep the MANIFEST file itself in the version control system as it is a generated file.

The command that creates the MANIFEST file is make manifest in case of ExtUtils::MakeMaker and it is perl Build manifes in case of Module::Build.