I have no clue of what you're talking about! AFAIKT nothing changed in this matter...
[EDIT]:
Actually i Do see your point now. Try changing these lines in the configuration.inc.php file:
...
// Destination for generated form drafts and panel drafts
define ('__FORM_DRAFTS__', _SUBDIRECTORY_ . '/drafts');
define ('__PANEL_DRAFTS__', _SUBDIRECTORY_ . '/drafts/dashboard');
...
To:
...
// Destination for generated form drafts and panel drafts
define ('__FORM_DRAFTS__', _SUBDIRECTORY_ . '/drafts/generated');
define ('__PANEL_DRAFTS__', _SUBDIRECTORY_ . '/drafts/dashboard/generated');
...
Then Re-CodGen, copy out what you need (as before ?) and note your changes remain untouched after successive code generations...
PS: Haven't actually tried this yet...