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cruft: update

- Migrate rules from .cursor/rules/ and .github/instructions/ to
  .claude/rules/
- Update all agent and skill files
- Add new workflows: flatpak, markdownlint, prettier, spelling
- Update existing workflows (appimage, codeql, publish, pyinstaller,
  qa, release, tests)
- Add ty type checker to dev dependencies
- Bump mypy to 1.20.0, ruff to 0.15.9, click to 8.3.2
- Add hatch build targets configuration
- Replace snapcraft.yaml with sh.tat.upkeep.yml (Flatpak manifest)
- Update Keep a Changelog link to 1.1.1
- Update pre-commit hooks, dependabot, and VS Code settings
- Update AGENTS.md, CLAUDE.md, README.md, CITATION.cff
- Add DOC201 and S101 to test Ruff ignore list
- Fix DOC201 warnings in decorators and utils.misc
- Add ty ignore comment in commands.kernel
- Modernise minenv() with functools.cache and dict comprehension
- Add context_settings to kernel_command click.command() call
- Update Yarn to 4.13.0, update yarn.lock and uv.lock

Signed-off-by: Andrew Udvare <audvare@gmail.com>

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