Edited Issue: File conflict dialog is open for loose files in projects, where overwrite option does not function [3086]

repro steps:
1. create a new class library project in VB, at the root of the project, add a class1.cs file as loose file (not referenced by the project)
2. install attached package

Expected: file conflict dialog does not pop up for class1.cs, which is the behavior for NuGet 2.2


Actual: dialog did pop up, choose overwrite option did not actually overwrite the file.


Below is the output on PMC for install the package that also illustrate the problem:

File 'class1.cs' already exists in project 'ClassLibrary2'. Do you want to overwrite it?
[Y] Yes [A] Yes to All [N] No [L] No to All [?] Help (default is "N"):__y__
Overwrite existing file 'class1.cs'.
__'class1.cs' already exists. Skipping...__
Successfully added 'LooseFileOverwrite 1.0.0' to ClassLibrary2.