[Win 4.9.1] Git never actually commits

I seem to be unable to use the Git source control plugin. I have a repo set up properly, but whenever I try to complete the "Submit to Source Control’ command, I get a heap of errors:

SourceControl: Info On branch master
SourceControl: Info Your branch is up-to-date with 'origin/master'.
SourceControl: Info Changes not staged for commit:
SourceControl: Info   (use "git add <file>..." to update what will be committed)
SourceControl: Info   (use "git checkout -- <file>..." to discard changes in working directory)
SourceControl: Info    modified:   Unreal Projects/Demo/Intermediate/CachedAssetRegistry.bin
SourceControl: Info    modified:   Unreal Projects/Demo/Saved/Config/Windows/EditorPerProjectUserSettings.ini
SourceControl: Info    modified:   Unreal Projects/Demo/Saved/Config/Windows/Engine.ini
SourceControl: Info no changes added to commit (use "git add" and/or "git commit -a")
SourceControl: Info fatal: D:/Program Files/Epic Games/4.9/Engine/Content/ArtTools/RenderToTexture/Blueprints/PhysMesh.uasset: 'D:/Program Files/Epic Games/4.9/Engine/Content/ArtTools/RenderToTexture/Blueprints/PhysMesh.uasset' is outside repository
SourceControl: Info fatal: D:/Program Files/Epic Games/4.9/Engine/Content/ArtTools/RenderToTexture/Enums/EFloatTypes.uasset: 'D:/Program Files/Epic Games/4.9/Engine/Content/ArtTools/RenderToTexture/Enums/EFloatTypes.uasset' is outside repository
SourceControl: Info fatal: D:/Program Files/Epic Games/4.9/Engine/Content/ArtTools/RenderToTexture/Macros/RenderToTextureMacros.uasset: 'D:/Program Files/Epic Games/4.9/Engine/Content/ArtTools/RenderToTexture/Macros/RenderToTextureMacros.uasset' is outside repository
SourceControl: Info fatal: D:/Program Files/Epic Games/4.9/Engine/Content/ArtTools/RenderToTexture/MaterialFunctions/BoundingSphereBased_0-1_UVW.uasset: 'D:/Program Files/Epic Games/4.9/Engine/Content/ArtTools/RenderToTexture/MaterialFunctions/BoundingSphereBased_0-1_UVW.uasset' is outside repository
SourceControl: Info fatal: D:/Program Files/Epic Games/4.9/Engine/Content/ArtTools/RenderToTexture/Materials/MPC_R2T.uasset: 'D:/Program Files/Epic Games/4.9/Engine/Content/ArtTools/RenderToTexture/Materials/MPC_R2T.uasset' is outside repository
SourceControl: Info fatal: D:/Program Files/Epic Games/4.9/Engine/Content/ArtTools/RenderToTexture/Materials/Debug/M_2sidedLit.uasset: 'D:/Program Files/Epic Games/4.9/Engine/Content/ArtTools/RenderToTexture/Materials/Debug/M_2sidedLit.uasset' is outside repository 
[SNIP - there are dozens of similar messages]
SourceControl: Info fatal: D:/Program Files/Epic Games/4.9/Engine/Content/: 'D:/Program Files/Epic Games/4.9/Engine/Content/' is outside repository

This seems to happen regardless of how I try to interface with the Git server in UE4. If I access it through GitHub for Windows, I can work with it normally, but the ability to diff Blueprints, and the integration in general, means I’d really like to figure out what’s going on so my team and I can use Git from the UE4 editor.