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If you have access to the CLI you don't need a script. Linux has two commands, find and chmod, which let you do that. For example, changing all file permissions to 0644 and all folder permissions to 0755:

find /path/to/your/site/root -type f -exec chmod 0644 \{} \;
find /path/to/your/site/root -type d -exec chmod 0755 \{} \;

The only reason we added this feature to the web interface of Admin Tools is that people typically don't have access to CLI :)

Regarding DB repair, it's not possible to do it with a single command. You'd have to enter a MySQL command line, list the tables and then run a repair and an optimize command for each table separately. That's a 2N+1 complexity with N being the number of your tables. With N being between 50 and 100 on most sites that's a 15' error-prone manual task. Or a 15 second automated script. So it totally made sense writing a CLI script for it. On the other hand, fixing permissions is a 5 second manual task. There's no gain turning it into a script.