Stuff like: use build && EXTRACTONLY+="include/" is forbidden by PMS and unpredictable. In particular, some PMs will unconditionally return false here and *not* reevaluate the variable when USE is established. I think you really need to move this setting into a phase function. I'm sorry I didn't notice this earlier.
Assuming that there are other instances beyond just the "use build [...]", are you able to enumerate the ebuilds in question that have issues, so we don't have to go hunting (and potentially miss some)
WARNING: 'use' function invoked by sys-freebsd/freebsd-cddl-10.2 during metadata regeneration. WARNING: Please ensure upstream is aware of it and working to remove it. WARNING: 'use' function invoked by sys-freebsd/freebsd-lib-10.2-r1 during metadata regeneration. WARNING: Please ensure upstream is aware of it and working to remove it. WARNING: 'use' function invoked by sys-freebsd/freebsd-lib-10.2-r1 during metadata regeneration. WARNING: Please ensure upstream is aware of it and working to remove it. WARNING: 'use' function invoked by sys-freebsd/freebsd-rescue-10.2 during metadata regeneration. WARNING: Please ensure upstream is aware of it and working to remove it. WARNING: 'use' function invoked by sys-freebsd/freebsd-sbin-10.2 during metadata regeneration. WARNING: Please ensure upstream is aware of it and working to remove it. WARNING: 'use' function invoked by sys-freebsd/freebsd-share-10.2 during metadata regeneration. WARNING: Please ensure upstream is aware of it and working to remove it. WARNING: 'use' function invoked by sys-freebsd/freebsd-sources-10.2-r1 during metadata regeneration. WARNING: Please ensure upstream is aware of it and working to remove it. WARNING: 'use' function invoked by sys-freebsd/freebsd-ubin-10.2-r1 during metadata regeneration. WARNING: Please ensure upstream is aware of it and working to remove it. WARNING: 'use' function invoked by sys-freebsd/freebsd-ubin-10.2-r1 during metadata regeneration. WARNING: Please ensure upstream is aware of it and working to remove it. WARNING: 'use' function invoked by sys-freebsd/freebsd-usbin-10.2-r4 during metadata regeneration. WARNING: Please ensure upstream is aware of it and working to remove it. WARNING: 'use' function invoked by sys-freebsd/freebsd-usbin-10.2-r4 during metadata regeneration. WARNING: Please ensure upstream is aware of it and working to remove it.
commit 73a205d7991182e5d2e1f8135b8c1a4b7482ba4e Author: Yuta Satoh <nigoro@gentoo.gr.jp> Date: Mon Nov 23 20:56:34 2015 +0900 sys-freebsd: Move use call from global scope to pkg_setup. Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=566522
