Repository-wide formatting pass over src/ and tests/: sorted imports and
__all__ entries, dropped redundant `# -*- coding: utf-8 -*-` headers,
unquoted forward-reference annotations (safe under
`from __future__ import annotations`), merged nested `with` statements,
moved `Iterable` and friends from `typing` to `collections.abc`, and
removed `# noqa: F401` markers that no longer suppress anything.
No behavioural changes. Unit and integration suites show the same four
pre-existing failures before and after the pass.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
* Add `force_update` to `RepoContext` and propagate it through install/update flows
* Add `pkgmgr install --update` to force re-running installers even if the same CLI layer is already loaded
* Enhance `NixFlakeInstaller` to ensure correct outputs (pkgmgr + optional default for package-manager) and support refresh/upgrade with index-based fallback remove+reinstall
* Make Python/Makefile installers emit an “upgraded” marker when `force_update` is used
* Add E2E tests for “three times install” scenarios (makefile, nix, venv) with shared run helper
* Fix git safe.directory wildcard quoting in E2E shell runner and minor cleanup/reordering of imports/comments
https://chatgpt.com/share/693db0b4-6ea4-800f-b44a-f03939c7fb9e
