I'm trying to update one of my older solutions before adding some new features to it. When I go to update the packages, It skips many files because "it was modified". The files were never modified from there original content, but were recently checked out of source control. I'm doing this in the Package Manager Console. Here is the output of the session:
PM> update-package -projectname AnonymousFeedback
No updates available for 'Modernizr'.
Updating 'jQuery.UI.Combined' from version '1.8.13' to '1.8.17' in project 'AnonymousFeedback'.
Skipping 'Content\themes\base\jquery.ui.accordion.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.all.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.autocomplete.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.base.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.button.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.core.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.datepicker.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.dialog.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.progressbar.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.resizable.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.selectable.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.slider.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.tabs.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.theme.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.accordion.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.all.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.autocomplete.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.base.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.button.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.core.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.datepicker.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.dialog.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.progressbar.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.resizable.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.selectable.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.slider.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.tabs.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.theme.css' because it was modified.
Skipping 'Scripts\jquery-ui-1.8.13.js' because it was modified.
Skipping 'Scripts\jquery-ui-1.8.13.min.js' because it was modified.
Successfully removed 'jQuery.UI.Combined 1.8.13' from AnonymousFeedback.
Successfully installed 'jQuery.UI.Combined 1.8.17'.
'Content\themes\base\jquery.ui.theme.css' already exists. Skipping...
'Content\themes\base\jquery.ui.tabs.css' already exists. Skipping...
'Content\themes\base\jquery.ui.slider.css' already exists. Skipping...
'Content\themes\base\jquery.ui.selectable.css' already exists. Skipping...
'Content\themes\base\jquery.ui.resizable.css' already exists. Skipping...
'Content\themes\base\jquery.ui.progressbar.css' already exists. Skipping...
'Content\themes\base\jquery.ui.dialog.css' already exists. Skipping...
'Content\themes\base\jquery.ui.datepicker.css' already exists. Skipping...
'Content\themes\base\jquery.ui.core.css' already exists. Skipping...
'Content\themes\base\jquery.ui.button.css' already exists. Skipping...
'Content\themes\base\jquery.ui.base.css' already exists. Skipping...
'Content\themes\base\jquery.ui.autocomplete.css' already exists. Skipping...
'Content\themes\base\jquery.ui.all.css' already exists. Skipping...
'Content\themes\base\jquery.ui.accordion.css' already exists. Skipping...
Successfully added 'jQuery.UI.Combined 1.8.17' to AnonymousFeedback.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.accordion.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.all.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.autocomplete.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.base.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.button.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.core.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.datepicker.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.dialog.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.progressbar.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.resizable.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.selectable.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.slider.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.tabs.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.theme.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.accordion.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.all.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.autocomplete.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.base.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.button.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.core.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.datepicker.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.dialog.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.progressbar.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.resizable.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.selectable.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.slider.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.tabs.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.theme.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Scripts\jquery-ui-1.8.13.js' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Scripts\jquery-ui-1.8.13.min.js' because it was modified.
The directory is not empty.
Successfully uninstalled 'jQuery.UI.Combined 1.8.13'.
Updating 'jQuery.Validation' from version '1.8.1' to '1.9' in project 'AnonymousFeedback'.
Skipping 'Scripts\jquery.validate-vsdoc.js' because it was modified.
Skipping 'Scripts\jquery.validate.js' because it was modified.
Skipping 'Scripts\jquery.validate.min.js' because it was modified.
Successfully removed 'jQuery.Validation 1.8.1' from AnonymousFeedback.
Successfully installed 'jQuery.Validation 1.9'.
'Scripts\jquery.validate-vsdoc.js' already exists. Skipping...
'Scripts\jquery.validate.min.js' already exists. Skipping...
'Scripts\jquery.validate.js' already exists. Skipping...
Successfully added 'jQuery.Validation 1.9' to AnonymousFeedback.
Skipping 'jQuery.Validation.1.8.1\Content\Scripts\jquery.validate-vsdoc.js' because it was modified.
Skipping 'jQuery.Validation.1.8.1\Content\Scripts\jquery.validate.js' because it was modified.
Skipping 'jQuery.Validation.1.8.1\Content\Scripts\jquery.validate.min.js' because it was modified.
The directory is not empty.
Successfully uninstalled 'jQuery.Validation 1.8.1'.
Updating 'jQuery' from version '1.6.1' to '1.7.1' in project 'AnonymousFeedback'.
Skipping 'Scripts\jquery-1.6.1-vsdoc.js' because it was modified.
Skipping 'Scripts\jquery-1.6.1.js' because it was modified.
Skipping 'Scripts\jquery-1.6.1.min.js' because it was modified.
Successfully removed 'jQuery 1.6.1' from AnonymousFeedback.
Successfully installed 'jQuery 1.7.1'.
Successfully added 'jQuery 1.7.1' to AnonymousFeedback.
Skipping 'jQuery.1.6.1\Content\Scripts\jquery-1.6.1-vsdoc.js' because it was modified.
Skipping 'jQuery.1.6.1\Content\Scripts\jquery-1.6.1.js' because it was modified.
Skipping 'jQuery.1.6.1\Content\Scripts\jquery-1.6.1.min.js' because it was modified.
Skipping 'jQuery.1.6.1\Tools\jquery-1.6.1-vsdoc-para.js' because it was modified.
The directory is not empty.
Successfully uninstalled 'jQuery 1.6.1'.
Updating 'log4netconf' from version '2011.5.10.5' to '2011.11.11.1' in project 'AnonymousFeedback'.
Successfully removed 'log4netconf 2011.5.10.5' from AnonymousFeedback.
Successfully removed 'log4net 1.2.10' from AnonymousFeedback.
Successfully installed 'log4net 1.2.11'.
Successfully added 'log4net 1.2.11' to AnonymousFeedback.
Successfully installed 'log4netconf 2011.11.11.1'.
Successfully added 'log4netconf 2011.11.11.1' to AnonymousFeedback.
Setting log4net.config to alway copy to output directory.
Updating 'ToolBox' from version '2011.6.2.6565' to '2011.12.14.7977' in project 'AnonymousFeedback'.
Successfully removed 'ToolBox 2011.6.2.6565' from AnonymousFeedback.
Successfully installed 'ToolBox 2011.12.14.7977'.
Successfully added 'ToolBox 2011.12.14.7977' to AnonymousFeedback.
No updates available for 'log4net'.
Comments: Ah, I think I found it? http://nuget.codeplex.com/workitem/278
PM> update-package -projectname AnonymousFeedback
No updates available for 'Modernizr'.
Updating 'jQuery.UI.Combined' from version '1.8.13' to '1.8.17' in project 'AnonymousFeedback'.
Skipping 'Content\themes\base\jquery.ui.accordion.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.all.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.autocomplete.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.base.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.button.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.core.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.datepicker.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.dialog.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.progressbar.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.resizable.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.selectable.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.slider.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.tabs.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.theme.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.accordion.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.all.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.autocomplete.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.base.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.button.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.core.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.datepicker.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.dialog.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.progressbar.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.resizable.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.selectable.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.slider.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.tabs.css' because it was modified.
Skipping 'Content\themes\base\jquery.ui.theme.css' because it was modified.
Skipping 'Scripts\jquery-ui-1.8.13.js' because it was modified.
Skipping 'Scripts\jquery-ui-1.8.13.min.js' because it was modified.
Successfully removed 'jQuery.UI.Combined 1.8.13' from AnonymousFeedback.
Successfully installed 'jQuery.UI.Combined 1.8.17'.
'Content\themes\base\jquery.ui.theme.css' already exists. Skipping...
'Content\themes\base\jquery.ui.tabs.css' already exists. Skipping...
'Content\themes\base\jquery.ui.slider.css' already exists. Skipping...
'Content\themes\base\jquery.ui.selectable.css' already exists. Skipping...
'Content\themes\base\jquery.ui.resizable.css' already exists. Skipping...
'Content\themes\base\jquery.ui.progressbar.css' already exists. Skipping...
'Content\themes\base\jquery.ui.dialog.css' already exists. Skipping...
'Content\themes\base\jquery.ui.datepicker.css' already exists. Skipping...
'Content\themes\base\jquery.ui.core.css' already exists. Skipping...
'Content\themes\base\jquery.ui.button.css' already exists. Skipping...
'Content\themes\base\jquery.ui.base.css' already exists. Skipping...
'Content\themes\base\jquery.ui.autocomplete.css' already exists. Skipping...
'Content\themes\base\jquery.ui.all.css' already exists. Skipping...
'Content\themes\base\jquery.ui.accordion.css' already exists. Skipping...
Successfully added 'jQuery.UI.Combined 1.8.17' to AnonymousFeedback.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.accordion.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.all.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.autocomplete.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.base.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.button.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.core.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.datepicker.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.dialog.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.progressbar.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.resizable.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.selectable.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.slider.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.tabs.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.theme.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.accordion.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.all.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.autocomplete.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.base.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.button.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.core.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.datepicker.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.dialog.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.progressbar.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.resizable.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.selectable.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.slider.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.tabs.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Content\themes\base\jquery.ui.theme.css' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Scripts\jquery-ui-1.8.13.js' because it was modified.
Skipping 'jQuery.UI.Combined.1.8.13\Content\Scripts\jquery-ui-1.8.13.min.js' because it was modified.
The directory is not empty.
Successfully uninstalled 'jQuery.UI.Combined 1.8.13'.
Updating 'jQuery.Validation' from version '1.8.1' to '1.9' in project 'AnonymousFeedback'.
Skipping 'Scripts\jquery.validate-vsdoc.js' because it was modified.
Skipping 'Scripts\jquery.validate.js' because it was modified.
Skipping 'Scripts\jquery.validate.min.js' because it was modified.
Successfully removed 'jQuery.Validation 1.8.1' from AnonymousFeedback.
Successfully installed 'jQuery.Validation 1.9'.
'Scripts\jquery.validate-vsdoc.js' already exists. Skipping...
'Scripts\jquery.validate.min.js' already exists. Skipping...
'Scripts\jquery.validate.js' already exists. Skipping...
Successfully added 'jQuery.Validation 1.9' to AnonymousFeedback.
Skipping 'jQuery.Validation.1.8.1\Content\Scripts\jquery.validate-vsdoc.js' because it was modified.
Skipping 'jQuery.Validation.1.8.1\Content\Scripts\jquery.validate.js' because it was modified.
Skipping 'jQuery.Validation.1.8.1\Content\Scripts\jquery.validate.min.js' because it was modified.
The directory is not empty.
Successfully uninstalled 'jQuery.Validation 1.8.1'.
Updating 'jQuery' from version '1.6.1' to '1.7.1' in project 'AnonymousFeedback'.
Skipping 'Scripts\jquery-1.6.1-vsdoc.js' because it was modified.
Skipping 'Scripts\jquery-1.6.1.js' because it was modified.
Skipping 'Scripts\jquery-1.6.1.min.js' because it was modified.
Successfully removed 'jQuery 1.6.1' from AnonymousFeedback.
Successfully installed 'jQuery 1.7.1'.
Successfully added 'jQuery 1.7.1' to AnonymousFeedback.
Skipping 'jQuery.1.6.1\Content\Scripts\jquery-1.6.1-vsdoc.js' because it was modified.
Skipping 'jQuery.1.6.1\Content\Scripts\jquery-1.6.1.js' because it was modified.
Skipping 'jQuery.1.6.1\Content\Scripts\jquery-1.6.1.min.js' because it was modified.
Skipping 'jQuery.1.6.1\Tools\jquery-1.6.1-vsdoc-para.js' because it was modified.
The directory is not empty.
Successfully uninstalled 'jQuery 1.6.1'.
Updating 'log4netconf' from version '2011.5.10.5' to '2011.11.11.1' in project 'AnonymousFeedback'.
Successfully removed 'log4netconf 2011.5.10.5' from AnonymousFeedback.
Successfully removed 'log4net 1.2.10' from AnonymousFeedback.
Successfully installed 'log4net 1.2.11'.
Successfully added 'log4net 1.2.11' to AnonymousFeedback.
Successfully installed 'log4netconf 2011.11.11.1'.
Successfully added 'log4netconf 2011.11.11.1' to AnonymousFeedback.
Setting log4net.config to alway copy to output directory.
Updating 'ToolBox' from version '2011.6.2.6565' to '2011.12.14.7977' in project 'AnonymousFeedback'.
Successfully removed 'ToolBox 2011.6.2.6565' from AnonymousFeedback.
Successfully installed 'ToolBox 2011.12.14.7977'.
Successfully added 'ToolBox 2011.12.14.7977' to AnonymousFeedback.
No updates available for 'log4net'.
Comments: Ah, I think I found it? http://nuget.codeplex.com/workitem/278