A little while ago, Yury Velikanov at Pythian blogged about a new feature in the RapidClone tool for EBS 12.1.2. In summary, Apps DBAs finally have the option to disable the startup of application services after cloning is complete. As Yury notes, this is big help, because there's often a long list of post-clone activities to perform prior to releasing a cloned system to users, many of which are best performed before starting the cloned system for the first time.
If you're not on 12.1.2, and would still like to accomplish this feat, it's pretty straightforward, as long as you're comfortable with editing the adcfgclone.pl script in $COMMON_TOP/clone/bin. It's easy and painless, honest! Just locate and comment out the line that executes adstrtal.sh. If you'd rather not do this manually with your favorite editor, here are two perl one-liners that will do the work for you, and preserve the original version of the script for reference:
For Release 11i:
perl -pi.old -e 's/(system.*adstr)/#$1/' adcfgclone.pl
For Release 12:
perl -pi.old -e 's/(runPipedCmd.*adstr)/#$1/' adcfgclone.pl
Depending on your EBS version and AD patch level, the line you're looking for may be slightly different. As with anything else I write about here, if you're foolish enough to follow along, at least do yourself the favor of testing things first.
On that note, it's occurred to me that the functionality Yury discusses in his blog post may be available in earlier EBS versions than 12.1.2, provided you're running a very recent AD Minipack. I'd welcome your comments confirming or disproving this theory, since I'm too lazy at the moment to dig through release notes on My Oracle Support to check.