Yes, we support deploying the SharePoint Connector on a Linux host.
You'll need to make sure that Confluence is configured to trust the SSL certificate from SharePoint (see http://confluence.atlassian.com/display/JIRA/Connecting+to+SSL+services).
Support NTLM when running on Linux is limited, though (in particular, NTLMv2 and Kerberos may be troublesome to get working). Since you're using HTTPS, you should look at downgrading the password encryption on your SharePoint site to NTLMv1 or HTTP Basic Authentication to ensure a trouble-free integration.
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