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An MSI program could report a successful uninstall and not actually be removed. Some registry UninstallStrings publish the Install verb (/I{GUID}) instead of Uninstall (/X{GUID}) -- a known authoring mistake. Making that silent ran a quiet repair instead of a removal: no window, exit code 0, nothing gone. The verb is corrected before Prune ever adds /qn.
A program's own uninstaller could genuinely open and still never be seen. Windows grants permission to steal the foreground once, to whichever process asks for it next -- not necessarily the uninstaller, and a self-relaunching installer can hand the real window to a different process than the one Prune started. Prune now actively searches for the window (its own, or any process it spawns) for a few seconds after launch and brings that exact one forward, rather than granting the permission once before anything exists to use it.
Nothing checked whether an uninstall actually worked. A successful spawn and a 0 exit code both say nothing reliable on their own -- Prune now re-reads the registry once the uninstaller exits, and if the program is still there, offers Forced Uninstall directly instead of moving on as if it had succeeded.
The scan-depth picker (Safe / Moderate / Advanced) no longer sits on the initial confirmation dialog. It is its own screen now, shown only once the real uninstaller has already run -- the confirmation dialog asks one question at a time.
The removal summary breaks a quarantined folder down into what was actually inside it -- folders, files, registry keys and registry values counted separately -- instead of rounding every quarantined item up to "1 item".