General Question about deployed application

hi,
When we deploy an application to the iAS, what is the place (that is... directory) where the application files are present?
I found it is available in two places. One is c:\iplanet\ias6\ias\Apps directory, where the application is present in a folder structure. Other is c:\iplanet\ias6\ias\jar directory where the application is present as jar.
Why in two places? And if i want to make any changes where should i do it? (I made change in index.html c:\iplanet\ias6\ias\Apps directory and it was effective. Then why to have the same application in jar directory too?).
thanks in advance,
desigan

<ias_home>\ias\jar is the directory that seems to be the staging area used by iasdeploy. The ear is finally exploded to the APPS directory from where it is used

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