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How do i take out the commented lines in the squid.conf file and make the newly created squid file the default config file for my squid proxy server ?

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How about sed :

sed -i.bak '/^#/d' /etc/squid/squid.conf

The original file will be saved as /etc/squid/squid.conf.bak. If you don't want to save the original file, use:

sed -i '/^#/d' /etc/squid/squid.conf

Or grep :

grep -v '^#' /etc/squid/squid.conf > /etc/squid/squid.conf.bak && mv /etc/squid/squid.conf.bak /etc/squid/squid.conf

I will not suggest you to just blindly remove all the lines starting with # as they may contain various important info/suggestions.

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