There are issues at: Unified Index with MySQL Full Text Search
Also, there should be warnings when site hits limitations of MySQL, that the admin needs to change to Zend_Lucene or ElasticSearch. Ideally, these warnings would come before hitting the limitations but this may not be easy to do.
Nelson (note to self): To make this bug actionable: these are the following actions. Many other things like excluding plugins by default are already done.
1) Make the logging use a different log file when triggered from the console vs the web (this will avoid any file perm problem).
2) Provide remarks box about including plugins in the admin panel.
3) Provide remarks box explaining that MySQL Full text search will only search first x characters of content (might affect large files in the file gallery for e.g.) - this is handled in item4641 already
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