dotnet tool manifest updates strip trailing newlines and BOM

`dotnet tool` commands (`install`, `update`, `uninstall`) perform an invasive rewrite of the `dotnet-tools.json` manifest that disregards original file formatting and encoding.

### Issues
1. **Trailing Newline Stripping:** Commands always strip the trailing newline. This causes "dirty diffs" in automated updates (Dependabot/Renovate) and breaks linting/EditorConfig rules requiring a final newline.
2. **BOM Removal:** Files saved as UTF-8 with BOM are rewritten as UTF-8 without BOM.
3. **UTF-16 Crash:** The CLI crashes with `Json parsing error: '0xFF' is an invalid start of a value` when reading UTF-16 LE manifests because `ToolManifestEditor.cs` uses `JsonDocument.Parse` on a raw stream.

### Technical Detail
The implementation in `src/Cli/dotnet/ToolManifest/ToolManifestEditor.cs` uses a strict "Read into Model -> Write from Model" pattern without capturing file metadata.

- `DeserializeLocalToolsManifest` uses `JsonDocument.Parse(jsonStream)` which lacks encoding detection.
- `ToJson` uses `Utf8JsonWriter` which does not append a final newline.
- `File.WriteAllText` is called without preserving the original encoding.

### Expected Behavior
The SDK should detect and preserve the existing file's encoding and trailing whitespace.