To clear out the wrap directory before DITA2Go copies files:
[Automation] WrapAndShip=Yes ; EmptyWrapPath = Yes (default, remove all files before copying) ; or No (leave old files in place in WrapPath directory) EmptyWrapPath=Yes
When EmptyWrapPath=Yes, provided WrapPath does not point to the project directory, DITA2Go deletes the entire contents of the WrapPath directory before copying files. However, if either of the following is true, DITA2Go does not delete anything, regardless of the value of EmptyWrapPath:
For HTML output types, if WrapPath points to the same directory as [Graphics]GraphPath, DITA2Go does not delete files unless both EmptyWrapPath and EmptyGraphPath are set to Yes; see §44.7 Placing graphics files for distribution.
When EmptyWrapPath=No, DITA2Go leaves the prior contents of the WrapPath directory in place. Orphaned and obsolete files from previous conversion runs could accumulate and find their way into current deliverables. For this reason, it is better to designate a directory for WrapPath that is different from the project directory, and set EmptyWrapPath=Yes; that way nothing important is lost, and nothing unwanted is delivered.
Note: EmptyWrapPath takes effect not only when WrapAndShip=Yes, but also when one of the following is true for the output type specified:
HTML Help: [Automation]CompileHelp=Yes
WinHelp: [Automation]CompileHelp=Yes
JavaHelp: [JavaHelpOptions]FTSCommand=path/to/indexer