参考  http://docs.oracle.com/cd/E26401_01/doc.122/e22954/T202991T531065.htm
Prepare the system for patching by running the following command to start a new patching cycle:  
$ adop phase=prepare  
 In this step, the patch fs APPL_TOP is synchronized with the run file system APPL_TOP. This can be done by either of two methods, the first is the default:
Method 1 - Identify the patches that were applied to the run APPL_TOP and apply them to the patch APPL_TOP. The following steps are performed automatically:
 The list of patches that need to be applied to the patch APPL_TOP are identified from the database.  
 The merged patches are applied using the adop utility.  
 This lightweight process is the preferred approach. The adop tool identifies the delta patches to be applied, and applies them silently to the current patch APPL_TOP. As this procedure only requires the application of delta patches, it is relatively fast compared to Method 2 (below).     
这种方法除了同步外，还做一些apply前的检查动作。
Method 2 - Create a new patch file system by cloning the run file system. 
This method is useful if the APPL_TOPs have become very unsynchronized (meaning that there would be a large number of delta patches to apply). It is a
heavyweight process, taking a backup of the entire current patch APPL_TOP and then cloning the run APPL_TOP to create a new patch APPL_TOP. A total 
of least 75 GB of free disk space is required. Also, you will need at least 25 GB of free space in your temporary directory (typically /tmp). This method is more
resource intensive, and will only be used when the state of the patch file system is unknown.
 The steps are as follows:
The fs_clone phase is run using the following command:
$ adop phase=fs_clone
This command must be invoked from the run file system, before the next prepare phase is run.

本文转自ITPUB博客tolywang的博客，原文链接：EBS R12.2 adop phase=prepare 与 adop phase=fs_clone 的关系与区别，如需转载请自行联系原博主。