I did a build publish to a mvc applications and See that packages.config is also deployed even though i did select "Only files required to run this application" in the properties. Can i safely remove this nuget package list file using wpp targets when deploying ?
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Yes you can remove it from the deployed application.
It is used by NuGet to keep a record of what NuGet packages are installed in a particular project.

Matt Ward
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7Why does the `Publish` place a copy of `packages.config` into the Publish directory? – fahadash Jun 02 '17 at 10:37
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By default, the build process copies all files from source to the destination directory. To exclude the file, right click the file, select properties and for Build Action choose 'None'.

R. Shan
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