These paradoxes don't ask to be solved. They exist to be seen and to be felt.
Perhaps the question is not what they mean, but what they expose in you as you search for meaning.
a file that explains how to understand a project.
If the README explains everything that can be explained about a project, should it explain itself?
a Unix command that kills processes by name.
If killall can terminate every process that can be terminated, can it terminate itself?
a file that defines which files Git should ignore.
If .gitignore can list every file that can be ignored, can it list itself?
a system that monitors other systems.
If Prometheus is a system that monitors all systems that are not monitored, who monitors Prometheus?
a document that grants permission to copy and distribute works.
If the LICENSE permits the redistribution of all redistributable works, does it permit its own?
a command that records a change.
If git commit --allow-empty records the absence of change, is it still a change?