This documentation relates to CiviCRM version 3.0. It's not maintained anymore.
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CiviCRM 3.0 Documentation

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Directories - Configure directories in your file system for temporary files, images, custom files and custom templates.

Click Directories which brings you to the Upload Directories page.
Default values are supplied for these upload directories the first time you access CiviCRM
based on the CIVICRM_TEMPLATE_COMPILEDIR file specified in civicrm.settings.php. If you need to modify the defaults, make sure that your web server has write access to the directories.

Indicate a path on your server or network for the item(s) you wish to setup - temporary files, images, custom files and/or custom templates.

For example, a temporary file path might look like this: /home/drupal/public_html/drupal/files/civicrm/upload/

Click Save to save your action or Cancel to cancel it.

If successful you will see the message "Your settings changes have been saved."

Custom Files Path

The current "default" setting for the Custom Files directory is below the default path for Temporary Files. This is potentially dangerous, as running the directoryCleanup debug action could delete all custom files. If you are using custom files, you should modify the path so it is NOT below your Temporary Files directory.

Custom Templates

To create custom templates, simply create a folder (ex. drupal/sites/all/civicrm_templates ).  And add the full system path into the custom templates section on the directories page.  

To modify a template (ex. civicrm/templates/CRM/History/Selector/Activity.tpl ) simply copy the path and file in your custom templates directory (ex. drupal/sites/all/civicrm_templates/CRM/History/Selector/Activity.tpl ) You can then modify the custom template.  CiviCRM searches your custom template directory and if it finds a template, it will use that instead of the stock template. 

Now when you upgrade CiviCRM your custom template will not be overwritten. 

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