I am developing an extension that implements a FileSystemProvider for which the query element of the uri is significant.

When an edited document is saved and VS Code detects that the target file is newer, VS Code correctly offers this notification:

But when the 'Compare' option is taken, the uri sent to the FSP has lost its query string.

The fault is here:

resourceToTextFile sequesters the query element to stash the original scheme when setting a new scheme. Later textFileToResource reverses this process, but in doing so it has lost the query element of the original uri.

I will submit a PR.