Basically MySQL is broken, it shouldn't ever close a connection that's open.
Various people have tried various workarounds. But using autoReconnect is not always semantically safe (you lose non-committed stuff).
Jackrabbit has implemented a workaround in 1.4 (https://issues.apache.org/jira/browse/JCR-940), but Nuxeo 5.1.6 uses 1.3.3.
See also http://wiki.magnolia-cms.com/display/WIKI/MySQL+Persistence for instance.
Your options are:
- upgrade the MySQL timeout to more that the default (8h), to avoid losing connections,
- restart Nuxeo from time to time, before the MySQL timeout,
- try to upgrade to Jackrabbit 1.4.* in Nuxeo 5.1.6, but there will probably be Nuxeo source code changes to do,
- upgrade Nuxeo to 5.2.RC1, but there are quite a number of other changes in Nuxeo so it's not a light operation,
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