test: Test all profiles (#2618)

* test: Test all profiles

Format every test files for every profiles and promote the output to:

    test/passing/refs.<profile name>/

The generated dune rules are written in a way that they can be included in the
profile directories.

The main reason for this change is to increase the coverage for the
default profile, which was barely tested.

This also avoids tests without a ref file, which are frustrating to work
with.

The '.ref' extension for output files is not dropped to avoid confusing
output files for input files.

Duplicate test cases are removed (eg. between source.ml and js_source.ml). THe
ocp-indent output is removed as it was not used anymore.
'verbose1.ml' test is removed because it doesn't work well with the
`--name` option.
The '.extra-deps' extension is also removed as it was not used.

The size of the dune file is also slightly reduced because the (package)
stanza could be removed.