Fix logging of expected exit codes

[pkwarren]

Both the lint and breaking change command are expected to return exit code 100 when issues are found. Update the logging to omit logging these cases so we only log warnings if a real failure occurs trying to run the Buf CLI.

Additionally, add a comment regarding file-level lint warnings (which are currently unsupported).

[github-actions[bot]]

Qodana Community for JVM

4 new problems were found

Inspection name	Severity	Problems
'Enum.values()' is recommended to be replaced by 'Enum.entries' since 1.9	🔶 Warning	2
Unstable API Usage	🔶 Warning	2

💡 Qodana analysis was run in the pull request mode: only the changed files were checked

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