...after all the personalizations I'd made to the HLT core...
Do you use Git(hub)?
Part of my goal this week is to try to get my local Arduino toolchain back to as close to the distribution defaults as possible again, then re-apply changes in a controlled and documented manner so I know what I've all changed.
Why go through all that trouble? Just use the latest version of WinAVR and be done with it.
I've been tempted to see about switching to avr-gcc and a more traditional make / compile / link process, though. But that feels like a bit more trouble anyway.
I'm not entirely sure what I'd be leaving behind and what I'd be gaining in the process.