With this change, it is possible to have a top-level object that does
not start at exactly the beginning of the file, allowing comments and
whitespace to exist.
Also add an empty conf file in the tests to verify that
it does not crash.
- split merge.conf into two files, one being standard JSON,
to ensure we can parse this
- ensure that key-value pairs are correctly overriden when
merging without the override. prefix
- remove context.modules, which is no longer needed there
- fix a typo with a stray ; character
