Use ~/.vcpkg/config instead of ~/vcpkg/config
MODIFY
src/vcpkg/userconfig.cpp
src/vcpkg/userconfig.cpp
@@ -35,7 +35,7 @@ namespace vcpkg
return get_localappdata() / "vcpkg" / "config";
#else
auto maybe_home = System::get_environment_variable("HOME");
- return fs::path(maybe_home.value_or("/var")) / "vcpkg" / "config";
+ return fs::path(maybe_home.value_or("/var")) / ".vcpkg" / "config";
#endif
}

Use ~/.vcpkg/config instead of ~/vcpkg/config