chore: clean packaging and development tooling

This commit modernizes the project's tooling and packaging without
changing the runtime code. It addresses dead workflows, obsolete
helper scripts, duplicated configuration, and stale developer docs.

Removed:
- .github/workflows/python-app.yml: targeted Python 3.12, referenced a
  non-existent requirements.txt, ran only flake8 with pytest commented out
- Makefile: hard-coded env/bin/python paths that do not work with uv
- run_tests.sh and run_tests.py: duplicated each other and referenced
  removed modules (test_exceptions, test_quick)
- sphinx/ and .readthedocs.yaml: the RTD config pointed to
  docs/source/conf.py while the sphinx tree lived under sphinx/source,
  so the build never worked and no docs were ever published
- docs/development/architecture.md, refactor-roadmap.md, and
  quality-and-utils.md: described the pre-cleanup proposal that
  included specs/exceptions/request_id, now contradicted by the code

Edited:
- pyproject.toml:
  - dropped the validation extra (Pydantic) — specs/ is gone
  - dropped the duplicated [tool.hatch.metadata].dependencies block
  - dropped the duplicated [dependency-groups].dev block
  - declared the wheel package explicitly via
    [tool.hatch.build.targets.wheel].packages
  - bumped pytest floor to >=8.0 (Python 3.13 compatible)
  - added richer classifiers (Development Status, audience, topic,
    Typing :: Typed), keywords, license file pointer, and a Changelog URL
- .github/workflows/python-pr-validation.yml: upgraded to
  actions/checkout@v4 and setup-python@v5, switched to astral-sh/setup-uv,
  removed obsolete architecture argument
- .github/dependabot.yml: added the github-actions ecosystem so
  workflow versions stay current

Added:
- pyvyos/py.typed: PEP 561 marker advertising the package as typed
- .pre-commit-config.yaml: neutral hooks only (whitespace, EOF, YAML/TOML
  syntax, large-file guard); no formatters or linters yet

Kept:
- docs/development/vyos_api/: JSON reference for the VyOS HTTPS API,
  useful for future contract tests

Tests still pass: 57/57.

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