Backend files that is effected in a cpanel server.

Apache
=======
/usr/local/apache
+ bin- apache binaries are stored here - httpd, apachectl, apxs
+ conf - configuration files - httpd.conf
+ cgi-bin
+ domlogs - domain log files are stored here
+ htdocs
+ include - header files
+ libexec - shared object (.so) files are stored here - libphp4.so,mod_rewrite.so
+ logs - apache logs - access_log, error_log, suexec_log
+ man - apache manual pages
+ proxy -
+ icons -

Init Script :/etc/rc.d/init.d/httpd - apache start script
Cpanel script to restart apache - /scripts/restartsrv_httpd

Exim
=====
Conf : /etc/exim.conf - exim main configuration file
/etc/localdomains - list of domains allowed to relay mail
Log : /var/log/exim_mainlog - incoming/outgoing mails are logged here
/var/log/exim_rejectlog - exim rejected mails are reported here
/exim errors are logged here
Mail queue: /var/spool/exim/input
Cpanel script to restart exim - /scripts/restartsrv_exim
Email forwarders and catchall address file - /etc/valiases/domainname.com
Email filters file - /etc/vfilters/domainname.com
POP user authentication file - /home/username/etc/domainname/passwd
catchall inbox - /home/username/mail/inbox
POP user inbox - /home/username/mail/domainname/popusername/inbox
POP user spambox - /home/username/mail/domainname/popusername/spam
Program : /usr/sbin/exim (suid - -rwsr-xr-x 1 root root )
Init Script: /etc/rc.d/init.d/exim

ProFTPD
========
Program :/usr/sbin/proftpd
Init Script :/etc/rc.d/init.d/proftpd
Conf: /etc/proftpd.conf
Log: /var/log/messages, /var/log/xferlog
FTP accounts file - /etc/proftpd/username - all ftp accounts for the domain are listed here

Pure-FTPD
=========
Program : /usr/sbin/pure-ftpd
Init Script :/etc/rc.d/init.d/pure-ftpd
Conf: /etc/pure-ftpd.conf
Anonymous ftp document root - /etc/pure-ftpd/ip-address

Frontpage Extensions
=================
Program - (Install): /usr/local/frontpage/version5.0/bin/owsadm.exe
Uninstall and then install for re-installations
FP files are found as _vti-bin, _vti-pvt, _vti-cnf, vti-log inside the public_html

Mysql
=======
Program : /usr/bin/mysql
Init Script : /etc/rc.d/init.d/mysql
Conf : /etc/my.cnf, /root/.my.cnf
Data directory - /var/lib/mysql - Where all databases are stored.
Database naming convention - username_dbname (eg: john_sales)
Permissions on databases - drwx 2 mysql mysql
Socket file - /var/lib/mysql/mysql.sock, /tmp/ mysql.sock

SSHD
======
Program :/usr/local/sbin/sshd
Init Script :/etc/rc.d/init.d/sshd
/etc/ssh/sshd_config
Log: /var/log/messages

Perl
====
Program :/usr/bin/perl
Directory :/usr/lib/perl5/5.6.1/

PHP
====

Program :/usr/local/bin/php, /usr/bin/php
ini file: /usr/local/lib/php.ini - apache must be restarted after any change to this file
php can be recomplied using /scripts/easyapache

Named(BIND)
============
Program: /usr/sbin/named
Init Script: /etc/rc.d/init.d/named
/etc/named.conf
db records:/var/named/
/var/log/messages

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Cpanel installation directory structure
=============================
/usr/local/cpanel
+ 3rdparty/ - tools like fantastico, mailman files are located here
+ addons/ - AdvancedGuestBook, phpBB etc
+ base/ - phpmyadmin, squirrelmail, skins, webmail etc
+ bin/ - cpanel binaries
+ cgi-sys/ - cgi files like cgiemail, formmail.cgi, formmail.pl etc
+ logs/ - cpanel access log and error log
+ whostmgr/ - whm related files

WHM related files
===============
/var/cpanel - whm files
+ bandwidth/ - rrd files of domains
+ username.accts - reseller accounts are listed in this files
+ packages - hosting packages are listed here
+ root.accts - root owned domains are listed here
+ suspended - suspended accounts are listed here
+ users/ - cpanel user file - theme, bwlimit, addon, parked, sub-domains all are listed in this files
+ zonetemplates/ - dns zone template files are taken from here

Common CPanel scripts
===================
cpanel/whm Scripts are located in /scripts/
+ addns - add a dns zone
+ addfpmail - Add frontpage mail extensions to all domains without them
+ addfpmail2 -Add frontpage mail extensions to all domains without them
+ addnetmaskips - Add the netmask 255.255.255.0 to all IPs that have no netmask
+ addnobodygrp - Adds the gorup nobody and activates security
+ addpop - add a pop account
+ addservlets - Add JSP support to an account (requires tomcat)
+ addstatus - (Internal use never called by user)
+ adduser - Add a user to the system
+ bandwidth - (OLD)
+ betaexim - Installs the latest version of exim
+ biglogcheck - looks for logs nearing 2 gigabytes in size
+ bsdcryptoinstall - Installs crypto on FreeBSD
+ bsdldconfig - Configures the proper lib directories in FreeBSD
+ bsdpkgpingtest - Tests the connection speed for downloading FreeBSD packages
+ buildbsdexpect - Install expect on FreeBSD
+ builddomainaddr - (OLD)
+ buildeximconf - Rebuilds exim.conf
+ buildpostgrebsd-dev - Installs postgresql on FreeBSD.
+ chcpass - change cpanel passwords
+ easyapache - recompile/upgrade apache and/or php
+ exim4 - reinstall exim and fix permissions
+ fixcommonproblems - fixes most common problems
+ fixfrontpageperm - fixes permission issues with Front Page
+ fixmailman - fixes common mailman issues
+ fixnamed - fixes common named issues
+ fixndc - fixes rndc errors with named
+ fixquotas - fixes quota problems
+ fullhordereset - resets horde database to a fresh one - all previous user data are lost
+ initquotas - initializes quotas
+ installzendopt - installs zend optimizer
+ killacct - terminate an account - make sure you take a backup of the account first
+ mailperm - fixes permission problems with inboxes
+ park - to park a domain
+ pkgacct - used to backup an account
+ restartsrv - restart script for services
+ restorepkg - restores an account from a backup file ( pkgacct file)
+ runlogsnow - update logs of all users
+ runweblogs - update stats for a particular user
+ securetmp - secures /tmp partition with options nosuexec and nosuid
+ suspendacct - suspends an account
+ unsuspendacct - unsuspends a suspended account
+ upcp - updates cpanel to the latest version
+ updatenow - updates the cpanel scripts
+ updateuserdomains - updates userdomain entries
Important cpanel/whm files
====================
/etc/httpd/conf/httpd.conf - apache configuration file
/etc/exim.conf - mail server configuration file
/etc/named.conf - name server (named) configuration file
/etc/proftpd.conf - proftpd server configuration file
/etc/pure-ftpd.conf - pure-ftpd server configuration file
/etc/valiases/domainname - catchall and forwarders are set here
/etc/vfilters/domainname - email filters are set here
/etc/userdomains - all domains are listed here - addons, parked,subdomains along with their usernames
/etc/localdomains - exim related file - all domains should be listed here to be able to send mails
/var/cpanel/users/username - cpanel user file
/var/cpanel/cpanel.config - cpanel configuration file ( Tweak Settings )*
/etc/cpbackup-userskip.conf -
/etc/sysconfig/network - Networking Setup*
/etc/hosts -
/var/spool/exim -
/var/spool/cron -
/etc/resolv.conf - Networking Setup--> Resolver Configuration
/etc/nameserverips - Networking Setup--> Nameserver IPs ( FOr resellers to give their nameservers )
/var/cpanel/resellers - For addpkg, etc permissions for resellers.
/etc/chkserv.d - Main >> Service Configuration >> Service Manager *
/var/run/chkservd - Main >> Server Status >> Service Status *
/var/log/dcpumon - top log process
/root/cpanel3-skel - skel directory. Eg: public_ftp, public_html. (Account Functions-->Skeleton Directory )*
/etc/wwwacct.conf - account creation defaults file in WHM (Basic cPanel/WHM Setup)*
/etc/cpupdate.conf - Update Config *
/etc/cpbackup.conf - Configure Backup*
/etc/clamav.conf - clamav (antivirus configuration file )
/etc/my.cnf - mysql configuration file
/usr/local/Zend/etc/php.ini OR /usr/local/lib/php.ini - php configuration file
/etc/ips - ip addresses on the server (except the shared ip) (IP Functions-->Show IP Address Usage )*
/etc/ipaddrpool - ip addresses which are free
/etc/ips.dnsmaster - name server ips
/var/cpanel/Counters - To get the counter of each users.
/var/cpanel/bandwidth - To get bandwith usage of domain