dotnet tool manifest updates strip trailing newlines and BOM

[Thomas-Shephard]

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.