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Comment: Replace http://marc.theaimsgroup.com/ with http://marc.info/

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Q1
Q1
How do I use OpenSSL to set up my own Certificate Authority (CA)?

Using OpenSSL to set up your own CA.

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Q2
Q2
OH NO! PORT 8005 is available for anyone on localhost to shutdown my tomcat!

See these 2 discussions.

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Q3
Q3
What about Tomcat running as root?

See these threads:

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Q4
Q4
How to I force all my pages to run under HTTPS?

Use security-constraint in web.xml.

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Q5
Q5
What is the default login for the manager and admin app?

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Fairly easily (wink) See the Setup page in the docs for your tomcat release, and read this mailing list post for a complete setup example with permissions etc.

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Yes, by numerous organizations and individuals, many times. Try this Google search and you'll see many references, guides, and analyses.

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