Ubuntu – Can’t connect to local MySQL server through socket ‘/var/run/thesqld/thesqld.sock’ (2) on subsequent connection through terminal

My sincere apologies for asking something that obviously has been answered before. The fact that I'm posting is that i would like to be absolutely sure since it's about a live server running currently.

This is what happened. I'm accidentally the sysadmin for a dedicated server. There is tomcat running on the machine and using mysql as database. I in the process of installing OpenCart happen to install curl, gd and mysql through

 apt-get install curl libcurl3 libcurl3-dev php5-curl
 restart apache2
 apt-get install php5-gd
 restart apache2
 apt-get install libapache2-mod-auth-mysql php5-mysql 
 restart apache2

I was connected before with mysql -u<username> -p and everything was just fine. Now it gives

ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)

Reading online and on ServerFault these are the facts:

#/var/lib# /etc/init.d/mysqld start
 -bash: /etc/init.d/mysqld: No such file or directory
#/var/lib# netstat -lntp | grep mysqld
tcp        0      0 0.0.0.0:3306            0.0.0.0:*               LISTEN      29570/mysqld  
#/var/lib# ps -ef | grep mysqld
root     13684 13580  0 09:25 pts/3    00:00:00 grep mysqld
root     29321     1  0  2011 ?        00:00:00 /bin/sh bin/mysqld_safe --user=mysql
mysql    29570 29321  0  2011 ?        03:58:46 /usr/local/mysql/bin/mysqld --basedir=/usr/local/mysql --datadir=/usr/local/mysql/data --plugin-dir=/usr/local/mysql/lib/plugin --user=mysql --log-error=/usr/local/mysql/data/server.host.com.err --pid-file=/usr/local/mysql/data/server.host.com.pid --socket=/tmp/mysql.sock --port=3306

This is how /etc/mysql/my.cnf looks like :

 [client]
 port            = 3306
 socket          = /var/run/mysqld/mysqld.sock

 [mysqld_safe]
 socket          = /var/run/mysqld/mysqld.sock
 nice            = 0

 [mysqld]
 user            = mysql
 socket          = /var/run/mysqld/mysqld.sock
 port            = 3306
 basedir         = /usr
 datadir         = /var/lib/mysql
 tmpdir          = /tmp
 skip-external-locking


 dpkg -l | grep mysql
 rc  libapache2-mod-auth-mysql       4.3.9-12ubuntu1              Apache 2 module for MySQL authentication
ii  libmysqlclient16                5.1.63-0ubuntu0.10.04.1      MySQL database client library
ii  mysql-common                    5.1.63-0ubuntu0.10.04.1      MySQL database common files (e.g. /etc/mysql
ii  php5-mysql                      5.3.2-1ubuntu4.17            MySQL module for php5

[EDIT]

apparently there are 2 my.cnf files

# ls -al /etc/my.cnf
-rw-r--r-- 1 root root 4715 2011-11-30 12:52 /etc/my.cnf
# ls -al /etc/mysql/my.cnf 
-rw-r--r-- 1 root root 3564 2012-06-11 14:11 /etc/mysql/my.cnf

below is the configuration of /etc/my.cnf

[client]
#password       = your_password
port            = 3306
socket          = /tmp/mysql.sock

# The MySQL server
[mysqld]
datadir         =/usr/local/mysql/data
port            = 3306
socket          = /tmp/mysql.sock

and the content of `/usr/local/mysql/ is below

/usr/local/mysql# ls -l
total 80
drwxr-xr-x  2 root  root  4096 2011-11-30 07:56 bin
-rw-r--r--  1 root  root 17987 2011-10-12 12:10 COPYING
drwx------ 11 mysql root  4096 2012-08-21 07:43 data
-rw-------  1 root  root   346 2011-11-30 13:09 DEADJOE
drwxr-xr-x  2 root  root  4096 2011-11-30 07:55 docs
drwxr-xr-x  3 root  root  4096 2011-11-30 07:55 include
-rw-r--r--  1 root  root  7604 2011-10-12 12:10 INSTALL-BINARY
drwxr-xr-x  3 root  root  4096 2011-11-30 07:56 lib
drwxr-xr-x  4 root  root  4096 2011-11-30 07:55 man
drwxr-xr-x 10 root  root  4096 2011-11-30 07:56 mysql-test
-rw-r--r--  1 root  root  2552 2011-10-12 12:10 README
drwxr-xr-x  2 root  root  4096 2011-11-30 07:56 scripts
drwxr-xr-x 27 root  root  4096 2011-11-30 07:56 share
drwxr-xr-x  4 root  root  4096 2011-11-30 07:56 sql-bench
drwxr-xr-x  2 root  root  4096 2011-11-30 07:55 support-files

There is no mysqld.sock in /var/run/mysqld and there is no /var/lib/mysql but there is
/usr/local/mysql/data containing mysql data and /tmp/mysqld.sock

So, what are my options here ?

Step 1 back up /etc/mysql/my.cnf

Step 2 remove /etc/mysql/my.cnf

Step 4 call /etc/init.d/mysql start (actually there is no mysql in /etc/init.d/ by mysql.server, am totally confused about this one)

So if i understand well. installing php5-mysql installed mysql-commons which created /etc/mysql/my.cnf meanwhile i already have /etc/my.cnf

Please advise on the issue as I don't want to make mistake and running commands with my own presumptions. Thanks for reading this.