Upgrade to El Capitan has broken MySQL and Apache
MySQL-5.6.14 was installed with a StartUpItem which is necessary to automatically start MySQL while booting. StartUpItems are deprecated meanwhile (and probably wasn't migrated therefore) and launch daemons are used instead.

To get your MySQL back do the following:


Create a soft link:

sudo ln -s /usr/local/mysql-5.6.14-osx10.7-x86_64 /usr/local/mysql

Check the permissions:

ls -laO /usr/local


The command should reveal:

...
lrwxr-xr-x   1 root  wheel  -  27 13 Apr 00:04 mysql -&gt; mysql-5.6.14-osx10.7-x86_64
drwxr-xr-x  17 root  wheel  - 578 13 Apr 00:05 mysql-5.6.14-osx10.7-x86_64
...

Create the file /Library/LaunchDaemons/com.oracle.oss.mysql.mysqld.plist with the following content:

&lt;?xml version="1.0" encoding="UTF-8"?&gt;
&lt;!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd"&gt;
&lt;plist version="1.0"&gt;
&lt;dict&gt;
    &lt;key&gt;Label&lt;/key&gt;             &lt;string&gt;com.oracle.oss.mysql.mysqld&lt;/string&gt;
    &lt;key&gt;ProcessType&lt;/key&gt;       &lt;string&gt;Interactive&lt;/string&gt;
    &lt;key&gt;Disabled&lt;/key&gt;          &lt;false/&gt;
    &lt;key&gt;RunAtLoad&lt;/key&gt;         &lt;true/&gt;
    &lt;key&gt;KeepAlive&lt;/key&gt;         &lt;true/&gt;
    &lt;key&gt;SessionCreate&lt;/key&gt;     &lt;true/&gt;
    &lt;key&gt;LaunchOnlyOnce&lt;/key&gt;    &lt;false/&gt;
    &lt;key&gt;UserName&lt;/key&gt;          &lt;string&gt;_mysql&lt;/string&gt;
    &lt;key&gt;GroupName&lt;/key&gt;         &lt;string&gt;_mysql&lt;/string&gt;
    &lt;key&gt;ExitTimeOut&lt;/key&gt;       &lt;integer&gt;600&lt;/integer&gt;
    &lt;key&gt;Program&lt;/key&gt;           &lt;string&gt;/usr/local/mysql/bin/mysqld&lt;/string&gt;
    &lt;key&gt;ProgramArguments&lt;/key&gt;
        &lt;array&gt;
            &lt;string&gt;/usr/local/mysql/bin/mysqld&lt;/string&gt;
            &lt;string&gt;--user=_mysql&lt;/string&gt;
            &lt;string&gt;--basedir=/usr/local/mysql&lt;/string&gt;
            &lt;string&gt;--datadir=/usr/local/mysql/data&lt;/string&gt;
            &lt;string&gt;--plugin-dir=/usr/local/mysql/lib/plugin&lt;/string&gt;
            &lt;string&gt;--log-error=/usr/local/mysql/data/mysqld.local.err&lt;/string&gt;
            &lt;string&gt;--pid-file=/usr/local/mysql/data/mysqld.local.pid&lt;/string&gt;
            &lt;string&gt;--port=3307&lt;/string&gt;
        &lt;/array&gt;
    &lt;key&gt;WorkingDirectory&lt;/key&gt;  &lt;string&gt;/usr/local/mysql&lt;/string&gt;
&lt;/dict&gt;
&lt;/plist&gt;


The file needs a trailing empty line/new line.

You may replace --port=3307 by --port=3306 depending on your previous configuration.
Change the permissions of the file:

sudo chown root:wheel /Library/LaunchDaemons/com.oracle.oss.mysql.mysqld.plist
sudo chmod 644 /Library/LaunchDaemons/com.oracle.oss.mysql.mysqld.plist

Load the launch daemon with

sudo launchctl load -w /Library/LaunchDaemons/com.oracle.oss.mysql.mysqld.plist



I strongly recommend to update to a newer version of MySQL.



Apache errors:

The error

AH00526: Syntax error on line 183 of /private/etc/apache2/httpd.conf:
Invalid command 'Order', perhaps misspelled or defined by a module not included in the server configuration


is related with the old Apache config (10.9) file you are using:

    &lt;Directory /&gt;
        Options FollowSymLinks
        AllowOverride None
        Order deny,allow
        Deny from all
    &lt;/Directory&gt;


In the new Apache config file (10.11) the section looks like this:

    &lt;Directory /&gt;
        AllowOverride none
        Require all denied
    &lt;/Directory&gt;


I recommend to setup Apache with a 2.4 (included in 10.11) config file.