I also noticed this issue. Furthermore, the output path is html-encoded, so e.g. spaces in de path are replaced by "%20".
Fortunately these bugs are easy to fix:
1. File IXmlTransform.cs, line 126:
this.baseUri = new Uri(new Uri(Directory.GetCurrentDirectory() + "/"), baseUri + "/");
Insert the following line just before the original line above:
if (string.IsNullOrEmpty(baseUri)) baseUri = ".";
If the given baseUri parameter is empty, then the Uri will be created with relativeUri equal to "./" (current directory) instead of "/" (root directory).This solves the issue of the output being saved relative to the root directory.
2. File OutputState.cs, line 67:
string outFile = outResolver.ResolveUri(null, href).AbsolutePath;
Replace "AbsolutePath" (encoded server path) with "LocalPath" (local file system path). This prevents the output path from being encoded.
Greetingz,
Zef