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So right now the load is not going to do what you want because it leaves the ignored files on disk.
So I made a work item that will request that option on the load 303187: Provide a "Pristine" option for load
I also made the work item for the build definition source control participant to support it too Support a "Pristine" load when configuring the source control of a build definition which would make the functionality available for use consistently in the plugin.
I also updated work item 296206: Make "Just accept and fetch from a build workspace" more full featured to make sure it includes this as well.
wrt to being able to have API to programmatically create/update/destroy build definitions, you will be interested in 272836: CCM Design SDK API. You might want to chime in there and identify the forum posts/workitems you have the describe your needs.