Fix CI: apt update on runner, file lock race condition

[mikekryjak]

The first error is:

Ign:4 https://security.ubuntu.com/ubuntu noble-updates/main amd64 libcurl4-openssl-dev amd64 8.5.0-2ubuntu10.7
Err:4 mirror+file:/etc/apt/apt-mirrors.txt noble-updates/main amd64 libcurl4-openssl-dev amd64 8.5.0-2ubuntu10.7
  404  Not Found [IP: 52.161.185.214 80]
E: Failed to fetch mirror+file:/etc/apt/apt-mirrors.txt/pool/main/c/curl/libcurl4-openssl-dev_8.5.0-2ubuntu10.7_amd64.deb  404  Not Found [IP: 52.161.185.214 80]
Fetched 4720 kB in 2s (2450 kB/s)
E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?

I tried to follow the error advice and add sudo apt-get update, which seems to resolve the same issue in xHermes. This PR adds it to xBOUT CI.

The second issue is where the tests hang on test_boutdataset.py::TestSaveRestart::test_to_restart. I reproduced the CI environment locally and reproduced the issue. Thanks to @dschwoerer's stack trace debug and the help of an LLM, I was then able to narrow this down to an unsafely loaded dataset in that test. This resolves the issue on my end at least....

[mikekryjak]

The tests were still failing locally, but intermittently. I made a bash script which loops the tests until they fail, and then prints a stack trace. I found another cause in another test inside test_boutdataset, where the dataset is opened and then quickly saved afterward. My LLM reckons that the lazy opening still kept a lock on the data files and clashed with the save operation. I made the fix here: 689613b

I also cherry picked @dschwoerer's timeout and stack trace from 62ab549.

While the CI continues, I will keep looping the tests locally to see if I can find more. If I do, I will make all file loads safe in this test file.

There is still the mystery of why it fails every time on CI and intermittently locally. My LLM thinks it could be because the runners are slow which could make timing and file locking issues worse.