How to inject files/commands into Docker bootstrap process?

Try a before_code: hook?

## The docker manager plugin allows you to one-click upgrade Discouse
## http://discourse.example.com/admin/docker
hooks:
  before_code:
    - file:
      path: /usr/share/ca-certificates/local/localca.crt
      contents:
        -----BEGIN CERTIFICATE-----
        MIICiDCCAg2gAwIBAgIQNfwmXNmET8k9Jj1Xm67XVjAKBggqhkjOPQQDAzCBhDEL
        MAkGA1UEBhMCVVMxFTATBgNVBAoTDHRoYXd0ZSwgSW5jLjE4MDYGA1UECxMvKGMp
        IDIwMDcgdGhhd3RlLCBJbmMuIC0gRm9yIGF1dGhvcml6ZWQgdXNlIG9ubHkxJDAi
        BgNVBAMTG3RoYXd0ZSBQcmltYXJ5IFJvb3QgQ0EgLSBHMjAeFw0wNzExMDUwMDAw
        MDBaFw0zODAxMTgyMzU5NTlaMIGEMQswCQYDVQQGEwJVUzEVMBMGA1UEChMMdGhh
        d3RlLCBJbmMuMTgwNgYDVQQLEy8oYykgMjAwNyB0aGF3dGUsIEluYy4gLSBGb3Ig
        YXV0aG9yaXplZCB1c2Ugb25seTEkMCIGA1UEAxMbdGhhd3RlIFByaW1hcnkgUm9v
        dCBDQSAtIEcyMHYwEAYHKoZIzj0CAQYFK4EEACIDYgAEotWcgnuVnfFSeIf+iha/
        BebfowJPDQfGAFG6DAJSLSKkQjnE/o/qycG+1E3/n3qe4rF8mq2nhglzh9HnmuN6
        papu+7qzcMBniKI11KOasf2twu8x+qi58/sIxpHR+ymVo0IwQDAPBgNVHRMBAf8E
        BTADAQH/MA4GA1UdDwEB/wQEAwIBBjAdBgNVHQ4EFgQUmtgAMADna3+FGO6Lts6K
        DPgR4bswCgYIKoZIzj0EAwMDaQAwZgIxAN344FdHW6fmCsO99YCKlzUNG4k8VIZ3
        KMqh9HneteY4sPBlcIx/AlTCv//YoT7ZzwIxAMSNlPzcU9LcnXgWHxUzI1NS41ox
        XZ3Krr0TKUQNJ1uo52icEvdYPy5yAlejj6EULg==
        -----END CERTIFICATE-----
    - exec:
      # etc etc etc
  after_code:
    - exec:
        cd: $home/plugins
        cmd:
          - mkdir -p plugins
          - git clone https://github.com/discourse/docker_manager.git

If you have a binary file, you can also cp it from /shared.

that file is /usr/share/ca-certificates/mozilla/thawte_Primary_Root_CA_-_G2.crt