Improve performance (#505) by only running auto-alt (and auto-perms)
when HEAD has changed after calling a git command, e.g. after committing
or pulling new changes.
Also use this new information to remove stale symlinks when an alt file
has been removed.
* Update base image to Ubuntu 24.10. This uses a python version where j2cli no
longer works when installed using pip so use the version from Ubuntu instead
which has been patched to work.
* Update shellcheck, pylint, pytest, isort, flake8, black and yamllint to the
latest versions. This closes#502.
* Use a longer expect timeout to fix tests failing when gpg is killed due to
this timeout.
* Explicitly flush gpg-agent's cached passwords to fix failing tests with
latest gnupg. Also clean up after tests to avoid having gpg-agents running
after the test (e.g. when running tests directly without docker).
