Neat; I wasn't aware of "well known" issues.
The easiest initial fix is to replace the one-at-a-time additions to core.a that end up doing 25 invocations for avr-gcc-ar...
(you can clump actual compiles, too, but last time I looked the IDE walked the directory and made individual decisions based on the type of each file. By the time you're building core.a, it would be easy to have a list of the .o files...)