[Code scan] Extend Dependabot coverage beyond GitHub Actions

This issue is a result of a Codex global code scan of deepmodeling/deepmodeling_sphinx at commit 156679fe55fc61e8ec3b1e9be8a45fde3567b9cb.

Problem

Dependabot currently updates only the `github-actions` ecosystem. Python package dependencies, documentation dependencies, and pre-commit hooks are declared elsewhere but do not receive automated update PRs.

Code references:

https://github.com/deepmodeling/deepmodeling_sphinx/blob/156679fe55fc61e8ec3b1e9be8a45fde3567b9cb/.github/dependabot.yml#L1-L6
https://github.com/deepmodeling/deepmodeling_sphinx/blob/156679fe55fc61e8ec3b1e9be8a45fde3567b9cb/pyproject.toml#L17-L24
https://github.com/deepmodeling/deepmodeling_sphinx/blob/156679fe55fc61e8ec3b1e9be8a45fde3567b9cb/docs/requirements.txt#L1-L6
https://github.com/deepmodeling/deepmodeling_sphinx/blob/156679fe55fc61e8ec3b1e9be8a45fde3567b9cb/.pre-commit-config.yaml#L3-L29

Impact

Runtime, docs, and linting dependencies can go stale without automated visibility, while workflow actions do get update coverage.

Suggested fix

Add Dependabot entries for `pip` dependency files and `pre-commit`, or document that these dependencies are intentionally maintained manually.