While editing scripts in MonoDevelop, user has created text templating "T4 Template" file, which was successfully added in file hierarchy in MonoDevelop. Then user switched to Unity editor and switched back to MonoDevelop. Project's solution is always updated with T4 Template files being removed from hierarchy in MonoDevelop.

Reproduced on all versions from 4.2.2f1 to 4.5.0a4;

Repro steps:
1. Create new project in Unity editor;
2. Create new C# script;
3. Open this new file from editor with MonoDevelop;
4. In MonoDevelop create T4 Template file (File -> New -> File -> Text Templating -> T4 template). Name file and tick the box below to add this file to project's "Assets" folder;
5. Observe that T4 template file appears in the solution;
6. Switch to Unity editor, wait while editor finishes script compiling, switch back to MonoDevelop, wait while it refreshes the solution.
7. Observe that T4 Template file has gone from solution hierarchy.

------------

Create T4 templates using the existing MonoDevelop add-in for this once the Monodevelop/Rest Integration is shipped. Also, Unity does not have direct support for handling T4 templates.

To use T4 templates, please use Xamarin Studio or Visual studio in a separate solution (.sln)