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If a TypeScript file has its build action set to "TypeScriptCompile", then the next time the project is loaded, it will be missing that TypeScript file. Unfortunately, its build action needs to be set to TypeScriptCompile for VS to automatically resolve dependencies between scripts. Note: This is with VS 2013 update 2.
In the iceproj file, this loads:
<Content Include="scripts\Controllers\MapController.ts">
<SubType>Content</SubType>
</Content>
This does not:
<TypeScriptCompile Include="scripts\Controllers\MapController.ts">
<SubType>TypeScriptCompile</SubType>
</TypeScriptCompile>
I do not experience this problem in a normal web project. Only AppBuilder projects.
In the iceproj file, this loads:
<Content Include="scripts\Controllers\MapController.ts">
<SubType>Content</SubType>
</Content>
This does not:
<TypeScriptCompile Include="scripts\Controllers\MapController.ts">
<SubType>TypeScriptCompile</SubType>
</TypeScriptCompile>
I do not experience this problem in a normal web project. Only AppBuilder projects.