Derby database directory missing service.properties file

Got this error after restarting Pipeline 2 yesterday:

```
ERROR XBM0A: The database directory '/var/opt/daisy-pipeline2/db' exists. However, it does not contain the expected 'service.properties' file. Perhaps Derby was brought down in the middle of creating this database. You may want to delete this directory and try creating the database again.
```

It may have occured after upgrading to `engine-1.9.11-20160414.134852-11.deb`, so maybe it's something with the way the DEB upgraded itself.

Relevant parts of the logs:
- [derby.txt](https://github.com/daisy/pipeline-framework/files/227538/derby.txt)
- [engine.txt](https://github.com/daisy/pipeline-framework/files/227539/engine.txt)

@bertfrees @capitancambio Should we do something special about this or is it out of our hands?

Start by reading the attached derby.txt and engine.txt logs and tracing the reported upgrade to engine-1.9.11-20160414.134852-11.deb. Determine whether the upgrade can leave /var/opt/daisy-pipeline2/db without service.properties, and document the required behavior or recovery path. Done means the cause and whether special handling is needed are established.

Written by the indexing model from the issue text.