Allow migration config to be overriden by command line options

[parshap]

Migration configuration specified in shepherd.yml should be overridable by command line options. This helps make migrations more reusable. For example, you could specify --adapter.search_query "org:nerdwallet filename:package.json react" to run a migration but with a different GitHub search query.

Notes:

• Some parts of shepherd.yml probably make less sense to be configurable by the command line, but for sake of flexibility and simplicity of implementation, we should probably just allow all keys to be overridable.
• Before/after "hooks" would probably be useful to run commands before or after the commands specified by the migration (e.g., --hooks.should_migrate.before "$(git show -s --format=%ct HEAD) <= $(date -d 'now - 100 days' +%s))".