scripts folder items all duplicated after convert-from-nuget

Description

I did a convert from nuget. My javascript packages were all duplicated. Unfortunately this is an old project and I have about 20 of these JS packages.

Repro steps

Please provide the steps required to reproduce the problem

1. Create an Web .cspoj.
2. Using nuget add bootstrap-dialog. a bootstrap-dialog.js will be placed in Scripts folder.
3. Convert from nuget to paket.

If possible then please create a git repository with a repro sample or attach a zip to the issue.

Expected behavior

There would be a single Scripts/bootstrap-dialog.js file on the disk, and a single reference to it in VS.

Actual behavior

There is a single file on disk, but the VS csproj has two references to it. I confrmed by looking within the csproj file.

Known workarounds

Manually edit the XML to remove the 2nd references. Unfortunately, deleting through VS deletes the file, so I can't do that.

Start by tracing the convert-from-nuget flow for a Web .cspoj project containing Scripts/bootstrap-dialog.js. Inspect how the conversion updates the VS csproj references, using the reported XML duplication as the reproduction case. Done means the file remains on disk and the csproj contains only one reference to it.