Apache supports two directives, SetEnvIf (mod_setenvif: http://httpd.apache.org/docs/mod/mod_setenvif.html#SetEnvIf ) and CustomLog (mod_log: http://www.apache.org/docs/mod/mod_log_config.html#customlog ).
This allows to filter the Alkaline's User-Agent into a different log file and remove Alkaline logs from the general log. For example:
SetEnvIf User-Agent "AlkalineBOT/.*" is-alkaline
CustomLog alkaline-requests.log common env=is-alkaline
CustomLog access_log common env=!is-alkaline
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