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From experience, persistent connections never worked very well for us. Even using mysql_pclose() in PHP didn't always work 100%.
You are definately probably better off with normal connections for your site. Any important script however should use pconnect so that it won't "Lost conneciton to server during query" on you.
Also, if it is a lot of work to change the pconnect's to connects, you are definately not building your code in a modular fashion ;>....For instance I have a db.inc which is basically a DB wrapper...thus I would call open_db("update") or open_db("select") for instance, the actual mysql_connect is in db.inc =)
Makes modifying things a LOT easier.
In your case however, you can use "rep" to just replace like so:
rep -R 'mysql_pconnect' 'mysql_connect' *
from your basedir.
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