You can use MSDeploy with Web Publishing Pipeline to exclude files to be included in the package creation.
You can use something like this if you want to exclude for example App_Data folder from the deployed package
<Target Name="ExcludeApp_Data" DependsOnTarget="$(ExcludeApp_DataDependsOn)" Condition="$(ExcludeApp_Data)" >
<ItemGroup>
<ExcludeFromPackageFolders Include="App_Data">
<FromTarget>ExcludeApp_Data</FromTarget>
</ExcludeFromPackageFolders>
</ItemGroup>
</Target>
Somehow editor doesn't display the code properly.
The above gets generated inside the proj file when you configure the Package/Publish web. You can add your own target to get it done.
For example, if you want to exclude Scripts\jquery files from your build, create seperate ExcludeScriptFiles.wpp.targets file as below
<ItemGroup>
<ExcludeFromPackageFolders Include="Internal">
<FromTarget>ExcludeScriptFiles.wpp.targets</FromTarget>
</ExcludeFromPackageFolders>
<ExcludeFromPackageFiles Include="Scripts\jquery.js;xyz.js">
<FromTarget>ExcludeScriptFiles.wpp.targets </FromTarget>
</ExcludeFromPackageFiles>
</ItemGroup>
This is just a simple example to write your own target.
Hope this helps