Hi,
Yeah, this is a pain when developing an AMP .. in reality you only want this bootstrap to run once in the installed AMP, but whilst your are developing you want to be able to re-run this bean to add your changes.
The most obvious and time consuming way is to clear your dB and indexes out and re-install your AMP everytime you make a change to bootstrap.
Another, less painful, technique I use is to create a unit test that calls the bootstrap XML files by hand and re-uploads them, thus refreshing the repo and testing the updates to the bootstrap.
Have a look in the PHP module for an example of this. (PHPUpdateExamplesTest.java)
Cheers,
Roy