Upgraded to 5.1, now the duplicates finder projects are all failing

Upgraded from 4.5 to 5.1 over the weekend.
Everything is looking good except that all of our duplicate checking builds are failing.
This is the ,net duplicates finder.

Example:
This build is triggered by the successful build of one of our libraries.
This build does has a snapshot dependency to the triggering build.
Here is the log from the build:

[08:51:23]: Skip checking for changes - changes are already collected
[08:51:24]: Clearing temporary directory: C:\TFSProd\Team City Build Agents\Agent 99\temp\buildTmp
[08:51:24]: Checkout directory: C:\TFSProd\Team City Build Agents\Agent 99\work\b15602feb4c796b0
[08:51:24]: Updating sources: server side checkout... (5s)
[08:51:24]: [Updating sources: server side checkout...] Building incremental patch for VCS root: Sales.Main
[08:51:29]: [Updating sources: server side checkout...] Repository sources transferred
[08:51:30]: Searching for duplicates
[08:51:30]: Start process: C:\TeamCity\buildAgent\plugins\dotnet-dupfinder\bin\dupfinder.exe --show-stats --show-text --discard-cost=90 --debug --discard-literals --normalize-types --exclude-by-comment=generated "--exclude-code-regions=generated code" "--exclude-code-regions=Component Designer generated code" -e *\AssemblyInfo.cs -e *\TestCases\* -e **/*.Generated.cs -i .\Appliances\Appliances.sln -o 05A1B22A-DE6E-49ae-AA30-DC52A074EF22\result.xml
[08:51:30]: in: C:\TFSProd\Team City Build Agents\Agent 99\work\b15602feb4c796b0
[08:51:30]: JetBrains Duplicates Finder for .NET. Version 2.0.120.0
[08:51:30]: Running in 32-bit mode
[08:51:36]: DEBUG Will output to 05A1B22A-DE6E-49ae-AA30-DC52A074EF22\result.xml
[08:51:36]: DEBUG Scanning file system
[08:51:36]: DEBUG Matched files:
[08:51:36]: DEBUG   none
[08:51:36]: FATAL Empty input file set. Terminating
[08:51:37]: Process exited with code 1
[08:51:37]: Build finished
1 comment

Solved by JetBrains.
Need to change how the solution is referenced in the duplicates runner.
Previously I used .\AAA\Solution.sln
need to change to AAA/Solution.sln

http://youtrack.jetbrains.net/issue/TW-11870

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