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The two "halves" of the SP software write to separate diagnostic log files by default, as configured by the shibd.logger and native.logger logging setup files. Some native logging messages will also be routed to the web server's own error log in the case of Apache.
Both "logger" files include several example categories of general interest that may be needed in specific cases in lieu of adjusting the root logging level.
Most of the interesting and relevant information will usually be found in the shibd.log, particularly SAML-related problems, Metadata issues, and most security issues.
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