What does this implement/fix?

Fix file comparison and add more debug logging during file comparison. So far, this should not have any negative consequences as all files we apply this function on will always differ somewhere before the end of the files when they are different (custom.list has the total number of lines on the end, dnsmasq.conf and pihole.toml have no multi-line options at the end).

Related issue or feature (if applicable): N/A

Pull request in docs with documentation (if applicable): N/A

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1. I have read and understood the contributors guide, as well as this entire template. I understand which branch to base my commits and Pull Requests against.
2. I have commented my proposed changes within the code.
3. I am willing to help maintain this change if there are issues with it later.
4. It is compatible with the EUPL 1.2 license
5. I have squashed any insignificant commits. (git rebase)

Checklist:

• The code change is tested and works locally.
• I based my code and PRs against the repositories developmental branch.
• I signed off all commits. Pi-hole enforces the DCO for all contributions
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• I have read the above and my PR is ready for review.