Committed output.json references index.html / cmec_output.log that are never produced (absent from manifest native)

## Summary

Committed regression `output.json` bundles reference two artefacts — `index.html` (top-level `index`) and `cmec_output.log` (`provenance.log`) — that the diagnostics never actually produce, so they are absent from the test case's `manifest.json` `native` block. The committed bundle and the native manifest are therefore out of sync: a consumer reading `output.json` would expect those files to exist, but `ref test-cases replay` has nothing to materialise for them.

Surfaced in review of #762 on `extratropical-modes-of-variability-nam/cmip7`:

> output.json still references index.html and cmec_output.log, but neither artefact is listed under native here. Add them to native, or remove those references from output.json.

## Root cause

`OutputBundle.create_template()` seeds every CMEC output bundle with hardcoded defaults:

`packages/climate-ref-core/src/climate_ref_core/pycmec/output.py:202-218`
```python
return {
OutputCV.INDEX.value: "index.html",
OutputCV.PROVENANCE.value: {
...
OutputCV.LOG.value: "cmec_output.log",
},
...
}
```

These defaults persist into the committed `output.json` even when the diagnostic writes neither file.

## Scope (committed baselines on `main`, 43 cases scanned)

| Artefact | Referenced by | Present in `native` |
|---|---|---|
| `cmec_output.log` | all 43 | **0** — never generated by any provider |
| `index.html` | all 43 | ilamb 20/20; **pmp 0/21, example 0/2** |

So `cmec_output.log` is a universal dangling reference, and `index.html` dangles for the 23 pmp + example cases (ilamb genuinely produces it). esmvaltool baselines (pending in #760) most likely follow the pmp/example pattern.

Read `packages/climate-ref-core/src/climate_ref_core/pycmec/output.py` at `OutputBundle.create_template()` and inspect the committed `output.json` files against each case's `manifest.json` `native` block. Run `ref test-cases replay` to check what is materialised; done means committed bundles no longer reference artefacts that the diagnostics do not produce.

Written by the indexing model from the issue text.