Fix database table indexes to better support actual queries in the API module

Migrated issue

Reported by: podarok

The query itself
SELECT ad.did FROM api_documentation ad WHERE ad.file_name = 'docs/html/de/db6/group__views__relationship__handlers.html' AND ad.branch_id = 3

time 22 seconds

Adding index fix the query

ALTER TABLE `api_documentation` ADD INDEX ( `branch_id` , `file_name` , `did` )