Since the p4 plugin has now set the ignore file to be .p4ignore/p4ignore.txt, and if you use that filename for your p4ignore, the "auto cleanup and sync" does not delete generated files if those generated files are in p4ignore.  

Request an additional option for "Auto cleanup and sync" that would add the "-I" option to the "p4 reconcile -w" command run by the plugin.

Workarounds:

1) alter view mappings to exclude .p4ignore/p4ignore.txt.

2)  use a different p4ignore filename