Malware scanners tend to focus on resident protection rather than intervention and clean-up, but Spybot has always had a clue there. Not only does Spybot explicitly support Bart PE as a formal scanning platform, it can also be aware of inactive registry hives, e.g. if you were to drop an ?infected hard drive into a Windows host system to clean it from there.
Bart has a plugin facility to integrate tools, and whenever there's a new version of a plugged-in tool, there may be changes required, or new unwanted behaviours to work around. Such is the case with the new Spybot 1.6
Spybot 1.6 plugin changes
A Bart plugin is a set of files that control how a program is integrated into a Bart CDR. Build-time instructions are defined in an .inf, menu integration via an nu2menu.xml, runtime control via a .cmd (if needed), and human documentation via an HTML file.
The .inf defines what files are to be copied to the CDR and where they are to be located, in the SourceDisksFiles and SourceDisksFolders sections. If you've used SourceDisksFiles to explicitly name every file from within Spybot 1.4 or 1.5 to be copied to CDR, and you then drop in the Spybot 1.6 file set and build a new Bart disk, then you'll find Spybot will fail to launch from the disk.
If so, you can fix this by adding a line to include sqlite3.dll, which is a new file not present in earlier versions of Spybot SD. Or you can use wildcard syntax to include all dll files, i.e. *.dll as files to be included.
Spybot 1.6 has a controversial new feature; it deletes Temp files when it starts up. This is "controlled" by a 6-second dialog box that appears as Spybot starts up (so if you start it and walk away, you'll miss it) and defaults to "Yes, delete temp files".
This is a bigger problem within the Bart environment, which often has troublesome graphics due to unrecognised display chipsets. In my first Bart session with Spybot 1.6, I expected the dialog, but it appeared with blank buttons. By the time I checked out what button was what, testing on another PC, the 6 seconds were up, and I'd lost material I'd have preferred to include in further malware scans.
There is a rather obscure fix for this, which I will add to my Bart plugin's .inf file, using one of the registry modification sections. If using the RunScanner plugin to launch Spybot (should not be required, as Spybot "knows" about such needs), then you'd want to delay the RunScanner redirection until this value had been read by Spybot after starting up - else it will look for it in the inactive (target) hives instead.