Error checking in PollRepositoriesJob

- skip if main project does not exist
- default branch of 'master' is not specified
Merge pull request #99 from square/rob/poll-repos-bug

Error checking in PollRepositoriesJob
Prevent from erroring on unrecognized submodules
Merge pull request #100 from square/jeversmann/submodule_sync

Prevent from erroring on unrecognized submodules
Put file reading logic into GitRepo
Log files from kochiku.yml and GitRepo cleaning