Unexpected merge conflicts after first sync

[pholleran]

Overview

After successfully syncing the first commit, all future commits create merge conflicts.

Environment

• gjtorikian/repository-sync running on a local (mac) machine or a CentOS 6.5 server in amazon (tried both)
• a repository testDotCom hosted on github.com
• a repository testEnterprise hosted on GitHub Enterprise
• ngrok running when testing on local machine

Steps to reproduce

• create a new repo on github.com testDotCom and initialize with a readme
  • repo consists of a single README.md with a single line of text
• clone the created repo locally
• create a new repo on GitHub Enterprise testEnterprise
• add GitHub Enterprise as a remote to the local repo and push
  • git remote add enterprise <path>
  • git push -u enterprise master
• set up webhooks (with secret token):
  • github.com: http://<ngrokOrAWSPath>/sync?sync_method=squash&dest_repo=org/testEnterprise&destination_hostname=HOST
  • Enterprise: http:///sync?sync_method=squash&dest_repo=<owner/Repo>
• verify webhooks are functioning using initial test payload
• Add a new line of text to README.md in the Enterprise repo (commit to master for simplicity's sake)
  • app runs as expected
• Add another new line of text to README.md in the Enterprise repo (commit to master)
  • Merge conflict

22:17:57 web.1    | 34.203.78.129 - - [06/May/2017:22:17:57 -0500] "POST /sync?dest_repo=pholleran%2FtestDotCom&sync_method=squash HTTP/1.1" 200 - 0.0027
22:18:02 worker.1 | I, [2017-05-06T22:18:02.308863 #27884]  INFO -- : New Cloner instance initialized
22:18:02 worker.1 | I, [2017-05-06T22:18:02.309639 #27884]  INFO -- : Cloning pholleran/testDotCom from github.com...
22:18:02 worker.1 | I, [2017-05-06T22:18:02.788834 #27884]  INFO -- : Adding remote for pH-Inc/testEnterprise on octodemo.com...
22:18:02 worker.1 | I, [2017-05-06T22:18:02.801196 #27884]  INFO -- : Fetching pH-Inc/testEnterprise...
22:18:03 worker.1 | I, [2017-05-06T22:18:03.353612 #27884]  INFO -- : Checking out update-1494127083
22:18:03 worker.1 | I, [2017-05-06T22:18:03.353775 #27884]  INFO -- : Running command git checkout -b update-1494127083
22:18:03 worker.1 | I, [2017-05-06T22:18:03.359626 #27884]  INFO -- : Result: Switched to a new branch 'update-1494127083'
22:18:03 worker.1 | 
22:18:03 worker.1 | I, [2017-05-06T22:18:03.359763 #27884]  INFO -- : Squashing pH-Inc/testEnterprise/master into update-1494127083...
22:18:03 worker.1 | I, [2017-05-06T22:18:03.359832 #27884]  INFO -- : Running command git merge --squash otherrepo-1494127082/master
22:18:03 worker.1 | I, [2017-05-06T22:18:03.366705 #27884]  INFO -- : Result: Auto-merging README.md
22:18:03 worker.1 | CONFLICT (content): Merge conflict in README.md
22:18:03 worker.1 | Squash commit -- not updating HEAD
22:18:03 worker.1 | Automatic merge failed; fix conflicts and then commit the result.
22:18:03 worker.1 | 
22:18:03 worker.1 | W, [2017-05-06T22:18:03.676443 #27884]  WARN -- : POST https://api.github.com/repos/pH-Inc/testEnterprise/issues: 404 - Not Found // See: https://developer.github.com/v3 (Octokit::NotFound)
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/octokit-3.7.0/lib/octokit/response/raise_error.rb:16:in `on_complete'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/faraday-0.9.1/lib/faraday/response.rb:9:in `block in call'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/faraday-0.9.1/lib/faraday/response.rb:57:in `on_complete'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/faraday-0.9.1/lib/faraday/response.rb:8:in `call'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/faraday-0.9.1/lib/faraday/rack_builder.rb:139:in `build_response'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/faraday-0.9.1/lib/faraday/connection.rb:377:in `run_request'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/faraday-0.9.1/lib/faraday/connection.rb:177:in `post'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/sawyer-0.6.0/lib/sawyer/agent.rb:94:in `call'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/octokit-3.7.0/lib/octokit/client.rb:339:in `request'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/octokit-3.7.0/lib/octokit/client.rb:144:in `post'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/octokit-3.7.0/lib/octokit/client/issues.rb:98:in `create_issue'
22:18:03 worker.1 | /Users/pholleran/github/repository-sync/lib/cloner.rb:182:in `report_error'
22:18:03 worker.1 | /Users/pholleran/github/repository-sync/lib/cloner.rb:163:in `run_command'
22:18:03 worker.1 | /Users/pholleran/github/repository-sync/lib/cloner.rb:227:in `squash'
22:18:03 worker.1 | /Users/pholleran/github/repository-sync/lib/cloner.rb:209:in `apply_sync_method'
22:18:03 worker.1 | /Users/pholleran/github/repository-sync/lib/cloner.rb:49:in `block (2 levels) in clone'
22:18:03 worker.1 | /Users/pholleran/github/repository-sync/lib/cloner.rb:43:in `chdir'
22:18:03 worker.1 | /Users/pholleran/github/repository-sync/lib/cloner.rb:43:in `block in clone'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/bundler-1.12.5/lib/bundler.rb:237:in `block in with_clean_env'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/bundler-1.12.5/lib/bundler.rb:447:in `with_env'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/bundler-1.12.5/lib/bundler.rb:237:in `with_clean_env'
22:18:03 worker.1 | /Users/pholleran/github/repository-sync/lib/cloner.rb:42:in `clone'
22:18:03 worker.1 | /Users/pholleran/github/repository-sync/lib/clone_job.rb:20:in `perform'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/resque-1.25.2/lib/resque/job.rb:227:in `perform'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/resque-1.25.2/lib/resque/worker.rb:250:in `perform'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/resque-1.25.2/lib/resque/worker.rb:189:in `block in work'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/resque-1.25.2/lib/resque/worker.rb:166:in `loop'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/resque-1.25.2/lib/resque/worker.rb:166:in `work'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/resque-1.25.2/lib/resque/tasks.rb:41:in `block (2 levels) in <top (required)>'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/task.rb:240:in `call'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/task.rb:240:in `block in execute'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/task.rb:235:in `each'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/task.rb:235:in `execute'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/task.rb:179:in `block in invoke_with_call_chain'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/2.2.0/monitor.rb:211:in `mon_synchronize'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/task.rb:172:in `invoke_with_call_chain'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/task.rb:201:in `block in invoke_prerequisites'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/task.rb:199:in `each'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/task.rb:199:in `invoke_prerequisites'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/task.rb:178:in `block in invoke_with_call_chain'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/2.2.0/monitor.rb:211:in `mon_synchronize'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/task.rb:172:in `invoke_with_call_chain'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/task.rb:165:in `invoke'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/application.rb:150:in `invoke_task'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/application.rb:106:in `block (2 levels) in top_level'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/application.rb:106:in `each'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/application.rb:106:in `block in top_level'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/application.rb:115:in `run_with_threads'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/application.rb:100:in `top_level'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/application.rb:78:in `block in run'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/application.rb:176:in `standard_exception_handling'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/lib/rake/application.rb:75:in `run'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/rake-10.3.2/bin/rake:33:in `<top (required)>'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/bin/rake:23:in `load'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/bin/rake:23:in `<top (required)>'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/bundler-1.12.5/lib/bundler/cli/exec.rb:63:in `load'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/bundler-1.12.5/lib/bundler/cli/exec.rb:63:in `kernel_load'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/bundler-1.12.5/lib/bundler/cli/exec.rb:24:in `run'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/bundler-1.12.5/lib/bundler/cli.rb:304:in `exec'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/bundler-1.12.5/lib/bundler/vendor/thor/lib/thor/command.rb:27:in `run'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/bundler-1.12.5/lib/bundler/vendor/thor/lib/thor/invocation.rb:126:in `invoke_command'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/bundler-1.12.5/lib/bundler/vendor/thor/lib/thor.rb:359:in `dispatch'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/bundler-1.12.5/lib/bundler/vendor/thor/lib/thor/base.rb:440:in `start'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/bundler-1.12.5/lib/bundler/cli.rb:11:in `start'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/bundler-1.12.5/exe/bundle:27:in `block in <top (required)>'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/bundler-1.12.5/lib/bundler/friendly_errors.rb:98:in `with_friendly_errors'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/lib/ruby/gems/2.2.0/gems/bundler-1.12.5/exe/bundle:19:in `<top (required)>'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/bin/bundle:23:in `load'
22:18:03 worker.1 | /Users/pholleran/.rbenv/versions/2.2.4/bin/bundle:23:in `<main>'
22:18:03 worker.1 | I, [2017-05-06T22:18:03.688065 #27884]  INFO -- : Cleaning up /var/folders/_t/shxbkdkj1f733g31x_ptnjfw0000gn/T/repository-sync20170506-27884-exe5gy

This also throws an API error in the mix ☝️ 22:18:03 worker.1 | W, [2017-05-06T22:18:03.676443 #27884] WARN -- : POST https://api.github.com/repos/pH-Inc/testEnterprise/issues: 404 - Not Found // See: https://developer.github.com/v3 (Octokit::NotFound) which I will reference in another issue

I would expect this to work without a problem, since adding another line shouldn't cause a merge conflict. I'm going to do what I can to figure this out, but would appreciate any 👀 from people more familiar with this app.