To remove comment lines under Linux, issue the following command:
# sed -e '/^#/d' -e '/^$/d' < squid.conf > newsquid.conf
Then, go can backup the original squid.conf file by copying it to say squidconf.bak:
# cp squid.conf squidconf.bak
And finally copying the new squid file to replace the original file as:
# cp newsquid.conf squid.conf
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