[Code scan] Pyright configuration excludes most format and plugin modules

This issue is part of a Codex global repository code scan.

The Pyright configuration only includes top-level `dpdata/*.py` files. Most implementation code lives in nested packages under `dpdata/formats`, `dpdata/plugins`, and `dpdata/md`, so the type-check workflow has limited coverage of the format/plugin code paths where most parsers and writers live.

Affected config:
https://github.com/deepmodeling/dpdata/blob/a7a50bfc096e1a65470af6f1c48152dc0275ec1c/pyproject.toml#L131-L134

Current configuration:

```toml
[tool.pyright]
include = [
"dpdata/*.py",
]
```

Repository shape from `git ls-files dpdata '*.py'` shows many nested modules outside this include pattern, including all parser/writer modules under `dpdata/formats` and registry modules under `dpdata/plugins`.

Suggested improvement: expand Pyright coverage to include nested package modules, or explicitly document why nested format/plugin modules are excluded.