We first saw this error when users were trying to install custom PEAR modules through cPanel:

/bin/pwd: cannot open directory `..’: Permission denied

This appears to be directly related to RHEL/CentOS5, according to cPanel’s blog entry here:

http://blog.cpanel.net/?p=50

Easy fix for cPanel:

/scripts/enablefileprotect

If you get this error when setting a quota:

touch: cannot touch `/aquota.user’: Permission denied.

Run:

chattr -ia /aquota.user

On some servers, mainly ones with larger disk arrays, you may experience the following error when attempting to set a quota or run the initial quota setup or fixquotas:

No filesystems with quota detected.

To fix this, you need to make sure the ‘usrquota’ option is located in /etc/fstab for any home partitions:

LABEL=/                 /                       ext3    defaults,usrquota,noatime        0 0

The either reboot, or remount:

mount -o remount /

Whenever your mainl server sends to or receives email from other servers, it broadcasts a greeting that looks somewhat like this:

220-your.hostname ESMTP Exim 4.68 #1 Tue, 06 May 2008 19:33:44 -0700
220-We do not authorize the use of this system to transport unsolicited,
220 and/or bulk e-mail.

To edit this greeting, you can edit the following section in /etc/exim.conf:

smtp_banner = "${primary_hostname} ESMTP Exim ${version_number}
#${compile_number} ${tod_full} n
 We do not authorize the use of this system to transport unsolicited, n
 and/or bulk e-mail."

Read the full tutorial at v-nessa.net:

http://www.v-nessa.net/2008/05/07/sexifying-whm-with-xml-api 

The XML API’s allow you to script many of the WHM reseller functions using perl or PHP.  This is particularly useful for external scripts and integration, or just giving your resellers access to perform certain functions without using WHM.

As of cPanel 11.23, proxy functionality has been restored internally without the need for the old cpanelproxy.net script that stopped working after 11.18.  Full instructions are here:

http://www.v-nessa.net/2008/07/26/setting-up-cpanel-proxies

In short:

1. Upgrade to cPanel 11.23 if you have not already
2. Enable the three proxy settings in WHM > Tweak Settings
3. Install mod_proxy if it is not already installed, preferably through EA3.  Vanessa at v-nessa.net includes instructions for installing the module separately if you do not want to reinstall Apache.