If I open the Package Content Editor for a package that has a customized packageboot.xml, I get a prompt stating that packageboot.xml differs from the local console client cache and will be overwritten. If I click Yes, the package boot file is overwritten with a default file, wiping out any customizations. I can cancel the dialog, but this prevents me from making any modifications to the package contents. The only way that I can find to change the contents of a package with custom package boot is to first export the XML from the Package Boot Editor, then update the files and finally re-import the XML.
Isn't there a better way?