BOA Aegir Octopus, APC disabled: Module's php files seem to be cached, changes are not reflected. Why?
Clearing Drupal cache may be not enough in this case. 

Since Redis is active by default, it may still cache some include paths, or there can be old paths still present in your system table, so you need to run the "Rebuild registry" task followed by "Flush all caches" task (the second is the same as running drush cc all on command line).   

If this still doesn't help, upgrade to latest BOA-2.0.6-dev (head), which includes recent APC 3.1.14 version to avoid this known APC bug.