JSON template negative indices silently map to trailing residues

## Description

Embedded JSON templates accept parallel `queryIndices` and `templateIndices` arrays. The parser checks only the upper bounds before indexing NumPy arrays and Python sequences. As a result, Python's negative-index semantics turn malformed mappings into valid-looking but incorrect template features:

- `queryIndices: [-1]` writes the mapped residue to the final query position.
- `templateIndices: [-2]` reads the second-to-last template residue.

`templateIndices: [-1]` is different: the parser explicitly treats it as the supported gap sentinel and should remain valid.

## Reproduction

Tested on current `main` at `4c355be4553512f72453ecbfb65e69f4c35d1413` with the repository's `examples/example_with_json_template/h_seq.json` mmCIF payload.

For a query of length 122 and a one-pair mapping:

```python
item["queryIndices"] = [-1]
item["templateIndices"] = [0]
result = featurizer.parse_json_templates([item], query_sequence)
```

Actual result:

```text
errors=[]
populated_query_indices=[121]
hit.indices_hit[-1]=0
```

Changing the pair to `queryIndices: [0]`, `templateIndices: [-2]` similarly returns no errors, populates query position 0 from the second-to-last template residue, and stores `-2` in `hit.indices_hit[0]`.

For comparison, the intended gap mapping `queryIndices: [0]`, `templateIndices: [-1]` leaves the query position unpopulated, and the normal mapping `0 -> 0` populates it with template residue 0.

## Expected behavior

A JSON template containing a negative query index or a template index below the `-1` gap sentinel should be rejected through `TemplateSearchResult.errors` instead of silently producing a corrupted mapping. `templateIndices == -1` should continue to represent a gap.

## Suggested fix

Validate the missing lower bounds before building or applying the mapping:

- every query index must be at least 0;
- every template index must be at least -1.

Keep the existing upper-bound behavior and add focused tests for query `-1`, template `-2`, the legal template `-1` gap, and a normal mapping.

Start at the parse_json_templates entry point and trace where queryIndices and templateIndices are bounds-checked and applied. Add focused coverage for query -1, template -2, legal template -1 gaps, and normal 0-to-0 mappings; done means invalid lower bounds populate TemplateSearchResult.errors without changing valid behavior.

Written by the indexing model from the issue text.