This specifically happens when using the msp430 overlay since it places MCU specific linker scripts (via installing the msp430mcu package) into /usr/msp430/lib/ldscripts so they can be automatically found by ld. However, I imagine this occurs for any arch since it's probably an internal directory to binutils. It would be nice to prevent these files from being removed on unmerge since it causes linking errors and user confusion when upgrading binutils.
After looking into this a bit, it appears to be caused by binutils-config when it is called in the toolchain-binutils_pkg_postrm function from the toolchain-binutils eclass. Specifically the following line from the binutils-config script is causing the issue: rm -rf "${ROOT}"/usr/${TARGET}/lib/ldscripts
should be all set now in the tree; thanks for the report! Commit message: Drop old upgrade logic that is only there for systems 4.5+ years old as it is causing issues with newer ones, and 4.5+ upgrade time is plenty http://sources.gentoo.org/sys-devel/binutils-config/binutils-config-3-r2.ebuild?rev=1.1 http://sources.gentoo.org/sys-devel/binutils-config/files/binutils-config-3?r1=1.6&r2=1.7
