Fix #79 (et al). Commandfile cache corrupt, commands go missing.

During bootstrap, we guess at which commandfiles to load from /profiles when the current command is not bootstrapping past DRUSH_BOOTSTRAP_DRUPAL_SITE. Unfortunately, we were doing this guessing always, not just for those special commands. This patch moves the guessing to within a conditional as it was before I introduced the bug in ac51e27d9448fda13ae8d864956d1fc665f86aef.

This should also make Drush a bit faster for sites that have big /profile directories that have many disabled modules.

Backports efdd5acd.
Remove a nonsense searchpath: 'sites/all/' . $path. Also remove a duplicate file_exists().