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I recently suffered through an issue with VSeWSS 1.3 that is very frustrating. When building and doing a "deploy" from inside VS.NET, if you run in to the following error, here are two options that worked for me.
The Error:
No language-neutral solution exists in the store.
The Theory:
Somehow the feature and or solution guid's become orphaned in the config/content db's
Simple Fix: (worked the first two times I saw this issue)
Run "setup -u" from the bin\debug\ directory of the project(s) which build a WSP. This uninstalls the Feature defined in the setup.bat file using the GUID generated by VSeWSS during the packaging.
Drastic Fix: (worked when Simple Fix did not)
Run the MissingFeature.exe utility and clean the SharePoint. The utility can be found here http://cid-06457d244696ab3c.skydrive.live.com/self.aspx/WSS/MissingFeature.exe.
Via Reflector: The MissingFeature.exe utility checks both the features in the Content DB and the local file system features GUIDs and notes missing file system GUIDs. This then uses "delete from dbo.Features where FeatureId = @FeatureId" to remove the orphaned items, so use this with caution.
For some details of the issues, here is a good description of the issue(s): http://menuke.spaces.live.com/blog/?fl=cat
Hopefully, this helps someone else!