Moved mypy to use local hook to unsilence it on missing dependencies

[jamesbraza]

Originally this PR added missing dependencies to pre-commit's mypy and removed the --ignore-missing-imports to unsilence this error for the future.

Then I hit errors like the below in this CI run:

src/paperqa/agents/__init__.py:16:1: error: Cannot find implementation or
library stub for module named "paperqa.version"  [import-not-found]
    from paperqa.version import __version__
    ^
src/paperqa/__init__.py:25:1: error: Cannot find implementation or library stub
for module named "paperqa.version"  [import-not-found]
    from paperqa.version import __version__
    ^

And this made me realize we just needed a local hook. So this PR then moved us to use local `mypy.

[Copilot]

Pull Request Overview

This PR improves the mypy type checking configuration in pre-commit by adding missing dependencies and removing the flag that silences import errors. This change ensures more comprehensive static type checking by making all necessary dependencies available to mypy and allowing it to report missing import issues.

• Removed --ignore-missing-imports flag to enable detection of missing imports
• Added --scripts-are-modules flag for better script handling
• Added four missing dependencies: PyPDF, pytest, pytest-asyncio, and pytest-subtests