Reduce duplication in the logs when errors occur in CLI commands

[henrymercer]

This PR reduces duplication in the logs when errors occur in CodeQL CLI invocations by taking the following strategy:

1. Try to find fatal errors in the CLI output.
2. If that fails, then rather than taking the whole stderr, just take the last line. Be explicit that we're taking the last line in the log message since it won't always be a good fit, and point customers to the full logs.
3. Fix a particularly bad case where during analyze we printed the error twice along with the stack trace. This resulted in us outputting the stderr three times along with a confusing stack trace.

Merge / deployment checklist

• Confirm this change is backwards compatible with existing workflows.
• Confirm the readme has been updated if necessary.
• Confirm the changelog has been updated if necessary.