Fix errors in base.command tests

[uwefladrich]

There are issues with the way base.command is tested, when pytest is running these tests in Github actions. Tests fail because some of the lines that the tests are checking are not appearing in the log capture. The whole problem is not really reproducible, tests run fine locally and sometimes even on Github.

[uwefladrich]

Things changed:

• test_command_ls does no longer rely on logging output and capture and saves stdout in the context instead
• same tests also waits two seconds to make sure file appears in the filesystem