Just changing to EAPI 6 and adding default to src_prepare() works for me.
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1fdd535b4a1161adb1eccf188aaa611ac8691240 commit 1fdd535b4a1161adb1eccf188aaa611ac8691240 Author: Matt Turner <mattst88@gentoo.org> AuthorDate: 2020-03-23 22:18:06 +0000 Commit: Matt Turner <mattst88@gentoo.org> CommitDate: 2020-03-23 22:19:04 +0000 www-apps/cgit: Use epatch_user Closes: https://bugs.gentoo.org/679700 Signed-off-by: Matt Turner <mattst88@gentoo.org> www-apps/cgit/cgit-1.2.3.ebuild | 2 ++ www-apps/cgit/cgit-9999.ebuild | 2 ++ 2 files changed, 4 insertions(+)