fwiw i did some testing of the make_linux_package script and everything seems to get constructed properly on master:

vagrant@vagrant-ubuntu-trusty-64:/vagrant$ tree /tmp/osquery_packaging
/tmp/osquery_packaging
└── prefix
    ├── etc
    │   ├── default
    │   │   └── osqueryd
    │   ├── init.d
    │   │   └── osqueryd
    │   └── osquery
    ├── usr
    │   ├── bin
    │   │   ├── osqueryctl
    │   │   ├── osqueryd
    │   │   └── osqueryi
    │   ├── lib
    │   │   └── systemd
    │   │       └── system
    │   │           └── osqueryd.service
    │   └── share
    │       └── osquery
    │           ├── certs
    │           │   └── certs.pem
    │           ├── osquery.example.conf
    │           └── packs
    │               ├── hardware-monitoring.conf
    │               ├── incident-response.conf
    │               ├── it-compliance.conf
    │               ├── osquery-monitoring.conf
    │               ├── osx-attacks.conf
    │               └── vuln-management.conf
    └── var
        ├── log
        │   └── osquery
        └── osquery

18 directories, 14 files