Okay I figured a way around the timeouts. Group your files together, and move all the *.amil files to the alice directory. Move like 5-7 files into the aiml directory and run botloaderinc.php
After you are done loading that, there is a link to continue processing...
From there, you move those 5-7 files back into the alice directory and move the next 5-7 files into the aiml directory. Run continue.
This will pretty much prevent timeouts. Keep repeating until you are done.
Note: KEEP STARTUP.XML in AIML NO MATTER WHAT.
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