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Directories you want to know about
/etc/[appname] – where [appname] is probably configured
/etc/init.d – where app startup/shutdown scripts are kept
/etc/rc[0-6].d – where the system looks for links to automatically run init.d scripts at startup or shutdown
/var/spool/cron/crontabs – where scheduled jobs are stored
/var/lib/mysql – where the MySQL db stores its binary data
/var/run – where apps store lockfiles - [appname].pid
/var/www – the default location for Apache websites
/tmp – where you put stuff you only need for a little while
/home – nobody cares about this but you
/dev – where all the devices live
/proc – where system info lives, and you can poke at the kernel