Based on the funny git results, I re-installed the packages:

3243aa899fcf2f09b910b7429eeae6205a71c379a45c0e8e31723836bb094163  apt_1.2.12~ubuntu16.04.1_amd64.deb
5b9a82b1dc1f82fc3655038336d099410d643d5188629aba475050d7f9bd99c3  apt-transport-https_1.2.12~ubuntu16.04.1_amd64.deb
25af186c488f2b7f31dcef15776bfe4dd1a7a3c98a1d378937f07365eb9aa95a  libapt-inst2.0_1.2.12~ubuntu16.04.1_amd64.deb
b84273b8bfddea9aa5be26b2dd2e7ed449503a93c92ac5522fdfa74ae6f61c22  libapt-pkg5.0_1.2.12~ubuntu16.04.1_amd64.deb


With these packages installed, apt-get update works as I expect:

sarnold@hunt:/mnt/ubuntu/.zfs/snapshot/rsync.30/pool/main/a/apt$ sudo apt-get update
Hit:1 http://mirrors.kernel.org/ubuntu xenial InRelease
Hit:2 http://mirrors.kernel.org/ubuntu xenial-updates InRelease                                                   
Hit:3 http://mirrors.kernel.org/ubuntu xenial-security InRelease                                                  
Ign:4 http://mirrors.kernel.org/ubuntu precise InRelease                                                          
Hit:5 http://security.debian.org jessie/updates InRelease                                                         
Hit:6 http://mirrors.kernel.org/ubuntu precise-updates InRelease                                                  
Hit:7 http://mirrors.kernel.org/ubuntu precise-security InRelease                                                 
Hit:8 http://mirrors.kernel.org/ubuntu precise-proposed InRelease                                                 
Hit:9 http://security.debian.org wheezy/updates InRelease                                                         
Ign:10 http://mirrors.kernel.org/ubuntu trusty InRelease                                                          
Hit:11 http://mirrors.kernel.org/ubuntu trusty-updates InRelease                                                  
Hit:12 http://mirrors.kernel.org/ubuntu trusty-security InRelease                                                 
Hit:13 http://mirrors.kernel.org/ubuntu trusty-proposed InRelease                                                 
Hit:14 http://mirrors.kernel.org/ubuntu xenial-proposed InRelease                                                 
Hit:15 http://mirrors.kernel.org/ubuntu yakkety InRelease                                                         
Ign:16 http://archive.canonical.com/ubuntu precise InRelease                                                      
Hit:17 http://ppa.launchpad.net/ci-train-ppa-service/stable-phone-overlay/ubuntu vivid InRelease                  
Hit:18 http://security.ubuntu.com/ubuntu xenial-security InRelease                                                
Hit:19 http://mirrors.kernel.org/ubuntu yakkety-updates InRelease                                                 
Hit:20 http://ftp.debian.org/debian unstable InRelease                                                            
Hit:21 http://mirrors.kernel.org/ubuntu yakkety-security InRelease                                                
Hit:22 http://mirrors.kernel.org/ubuntu yakkety-proposed InRelease                                                
Hit:23 http://mirrors.kernel.org/ubuntu zesty InRelease                                        
Hit:24 http://mirrors.kernel.org/ubuntu zesty-updates InRelease                                
Hit:25 http://mirrors.kernel.org/ubuntu zesty-security InRelease                                                  
Hit:26 http://mirrors.kernel.org/ubuntu zesty-proposed InRelease                                                  
Ign:27 http://archive.canonical.com/ubuntu trusty InRelease                                    
Hit:28 http://ppa.launchpad.net/snappy-dev/image/ubuntu vivid InRelease                                           
Hit:29 http://mirrors.kernel.org/ubuntu precise Release                                                           
Hit:30 http://ftp.debian.org/debian testing InRelease                                          
Hit:31 http://mirrors.kernel.org/ubuntu trusty Release                                         
Hit:32 http://archive.canonical.com/ubuntu xenial InRelease                                    
Hit:33 http://ppa.launchpad.net/ci-train-ppa-service/stable-phone-overlay/ubuntu xenial InRelease
Ign:34 http://ftp.debian.org/debian jessie InRelease                     
Hit:35 http://archive.canonical.com/ubuntu yakkety InRelease              
Hit:36 http://ftp.debian.org/debian jessie-updates InRelease              
Hit:37 http://archive.canonical.com/ubuntu zesty InRelease                
Ign:38 http://ftp.debian.org/debian wheezy InRelease                     
Hit:39 http://archive.canonical.com/ubuntu precise Release                
Hit:40 http://ftp.debian.org/debian wheezy-updates InRelease              
Hit:41 http://archive.canonical.com/ubuntu trusty Release                 
Hit:42 http://ftp.debian.org/debian jessie Release                       
Hit:43 http://ftp.debian.org/debian wheezy Release  
Reading package lists... Done                      
W: http://mirrors.kernel.org/ubuntu/dists/precise-updates/InRelease: Signature by key 630239CC130E1A7FD81A27B140976EAF437D05B5 uses weak digest algorithm (SHA1)
W: http://mirrors.kernel.org/ubuntu/dists/precise-security/InRelease: Signature by key 630239CC130E1A7FD81A27B140976EAF437D05B5 uses weak digest algorithm (SHA1)
W: http://mirrors.kernel.org/ubuntu/dists/precise-proposed/InRelease: Signature by key 630239CC130E1A7FD81A27B140976EAF437D05B5 uses weak digest algorithm (SHA1)
W: http://mirrors.kernel.org/ubuntu/dists/precise/Release.gpg: Signature by key 630239CC130E1A7FD81A27B140976EAF437D05B5 uses weak digest algorithm (SHA1)
W: http://archive.canonical.com/ubuntu/dists/precise/Release.gpg: Signature by key 630239CC130E1A7FD81A27B140976EAF437D05B5 uses weak digest algorithm (SHA1)


All the *InRelease* files looked fine:

sarnold@hunt:/var/lib/apt/lists$ for f in *InRelease* ; do apt-key  verify $f ; done
gpgv: Signature made Wed 09 Nov 2016 05:30:58 AM PST using DSA key ID 437D05B5
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key <email address hidden>"
gpgv: Signature made Wed 09 Nov 2016 05:30:58 AM PST using RSA key ID C0B21F32
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key (2012) <email address hidden>"
gpgv: Signature made Wed 09 Nov 2016 05:30:58 AM PST using DSA key ID 437D05B5
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key <email address hidden>"
gpgv: Signature made Wed 09 Nov 2016 05:30:58 AM PST using RSA key ID C0B21F32
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key (2012) <email address hidden>"
gpgv: Signature made Wed 16 Nov 2016 09:39:23 AM PST using RSA key ID C0B21F32
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key (2012) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 12:38:16 PM PST using RSA key ID 46925553
gpgv: Good signature from "Debian Archive Automatic Signing Key (7.0/wheezy) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 12:38:16 PM PST using RSA key ID 2B90D010
gpgv: Good signature from "Debian Archive Automatic Signing Key (8/jessie) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 12:39:39 PM PST using RSA key ID 46925553
gpgv: Good signature from "Debian Archive Automatic Signing Key (7.0/wheezy) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 12:39:39 PM PST using RSA key ID 2B90D010
gpgv: Good signature from "Debian Archive Automatic Signing Key (8/jessie) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 12:40:14 PM PST using RSA key ID 46925553
gpgv: Good signature from "Debian Archive Automatic Signing Key (7.0/wheezy) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 12:40:14 PM PST using RSA key ID 2B90D010
gpgv: Good signature from "Debian Archive Automatic Signing Key (8/jessie) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 12:38:14 PM PST using RSA key ID 46925553
gpgv: Good signature from "Debian Archive Automatic Signing Key (7.0/wheezy) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 12:38:14 PM PST using RSA key ID 2B90D010
gpgv: Good signature from "Debian Archive Automatic Signing Key (8/jessie) <email address hidden>"
gpgv: Signature made Sun 13 Nov 2016 01:14:06 AM PST using DSA key ID 437D05B5
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 11:47:14 AM PST using DSA key ID 437D05B5
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 12:21:53 PM PST using DSA key ID 437D05B5
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 01:25:35 AM PST using DSA key ID 437D05B5
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 01:25:35 AM PST using RSA key ID C0B21F32
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key (2012) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 11:47:14 AM PST using DSA key ID 437D05B5
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 11:47:14 AM PST using RSA key ID C0B21F32
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key (2012) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 12:21:53 PM PST using DSA key ID 437D05B5
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 12:21:53 PM PST using RSA key ID C0B21F32
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key (2012) <email address hidden>"
gpgv: Signature made Thu 21 Apr 2016 04:25:09 PM PDT using DSA key ID 437D05B5
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key <email address hidden>"
gpgv: Signature made Thu 21 Apr 2016 04:25:09 PM PDT using RSA key ID C0B21F32
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key (2012) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 03:33:29 PM PST using DSA key ID 437D05B5
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 03:33:29 PM PST using RSA key ID C0B21F32
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key (2012) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 01:25:35 AM PST using DSA key ID 437D05B5
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 01:25:35 AM PST using RSA key ID C0B21F32
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key (2012) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 10:35:05 AM PST using DSA key ID 437D05B5
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 10:35:05 AM PST using RSA key ID C0B21F32
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key (2012) <email address hidden>"
gpgv: Signature made Thu 13 Oct 2016 06:29:09 AM PDT using DSA key ID 437D05B5
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key <email address hidden>"
gpgv: Signature made Thu 13 Oct 2016 06:29:09 AM PDT using RSA key ID C0B21F32
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key (2012) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 02:58:32 PM PST using DSA key ID 437D05B5
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 02:58:32 PM PST using RSA key ID C0B21F32
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key (2012) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 01:25:35 AM PST using DSA key ID 437D05B5
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 01:25:35 AM PST using RSA key ID C0B21F32
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key (2012) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 11:53:31 AM PST using DSA key ID 437D05B5
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 11:53:31 AM PST using RSA key ID C0B21F32
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key (2012) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 01:57:37 PM PST using RSA key ID C0B21F32
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key (2012) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 03:33:29 PM PST using RSA key ID C0B21F32
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key (2012) <email address hidden>"
gpgv: Signature made Fri 21 Oct 2016 07:24:27 AM PDT using DSA key ID 437D05B5
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key <email address hidden>"
gpgv: Signature made Fri 21 Oct 2016 07:24:27 AM PDT using RSA key ID C0B21F32
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key (2012) <email address hidden>"
gpgv: Signature made Fri 21 Oct 2016 07:24:27 AM PDT using DSA key ID 437D05B5
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key <email address hidden>"
gpgv: Signature made Fri 21 Oct 2016 07:24:27 AM PDT using RSA key ID C0B21F32
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key (2012) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 12:36:15 PM PST using RSA key ID ECF1204C
gpgv: Good signature from "Launchpad PPA for CI Train PPA Service Team"
gpgv: Signature made Thu 17 Nov 2016 12:36:14 PM PST using RSA key ID ECF1204C
gpgv: Good signature from "Launchpad PPA for CI Train PPA Service Team"
gpgv: Signature made Fri 20 May 2016 04:39:04 AM PDT using RSA key ID FC42E99D
gpgv: Good signature from "Launchpad PPA for Snappy Developers"
gpgv: Signature made Thu 17 Nov 2016 01:40:55 PM PST using RSA key ID C857C906
gpgv: Good signature from "Debian Security Archive Automatic Signing Key (8/jessie) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 01:40:55 PM PST using RSA key ID 46925553
gpgv: Good signature from "Debian Archive Automatic Signing Key (7.0/wheezy) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 01:40:55 PM PST using RSA key ID C857C906
gpgv: Good signature from "Debian Security Archive Automatic Signing Key (8/jessie) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 01:40:55 PM PST using RSA key ID 46925553
gpgv: Good signature from "Debian Archive Automatic Signing Key (7.0/wheezy) <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 01:25:35 AM PST using DSA key ID 437D05B5
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key <email address hidden>"
gpgv: Signature made Thu 17 Nov 2016 01:25:35 AM PST using RSA key ID C0B21F32
gpgv: Good signature from "Ubuntu Archive Automatic Signing Key (2012) <email address hidden>"