Steps/best practices for server updating and maintenance?

[Andvari]

So I've had my private server up and running for a week or two now. It's been quite an educational journey! I've learned a good bit of MySQL, LUA, and a dash of Perl and C++ along the way. However I do have a few questions.

1. Server source. Once I have enabled bots, is the server_source/ folder utilized any longer at all? Or does the new server_source_bots/ directory effectively replace it entirely?
2. Updating server code. What's the intended way to handle this? None of the scripts in eqemu_server.pl update the code, correct? Running git fetch and git status in the source directory showed I was about 25 commits behind master, so that seems to indicate the source hadn't been updated since my initial install a couple weeks ago, despite having run the setup_bots command just a few days ago after editing some source code myself. So of course a git pull will update the source; I just wanted to check if that's the best way to go about things. This leads to my next question...
3. Compiling the updated source. In eqemu_server.pl, setup_bots seems to recompile source if it's updated. Is this the way to go? This question might belong in the appropriate Windows/Linux subforum. Let me know if so. I'm running the server on Linux.
4. Database updates. The two database update checker scripts in eqemu_server.pl - these seem to add some tables occasionally (when there are updated tables to be added of course). Do they do anything else? For example, if the PEQ database updated some zone points, do these scripts handle that? Or would that involve downloading the newest PEQ database? Speaking of that, do any of the scripts do that other than the new_server script? I've been saving all the MySQL commands I've run in an .sql file (disabling defiant, disabling Fabled creatures, fixing zone_point headings, etc.) and running the backup_player_tables script periodically, so in case I need to get a completely fresh database from PEQ, I can run all my custom commands quickly and easily and not lose any characters. Would this ever be necessary or do the update scripts grab everything new from new PEQ databases?
5. Last but not least, a little explanation of the two last commands in the Database submenu of the eqemu_server.pl script. What do these do? remove_duplicate_rules seems self explanatory, except why would there be duplicate rules? When would you ever need to run this? And what does aa_tables do? Clean slate AA data? I guess my question is the same as the previous one - when do you ever need to run this?

Hopefully these questions haven't been answered already elsewhere. I've looked around the forums, and like I said the server is running well after the various hurdles I've overcome in the past week or two. If it's not broke, don't fix it I guess! But I just wanted to get a better understanding of how all these things interrelate so I can handle server maintenance going forward the best way possible (maybe better/faster than what I'm currently doing).