documentation creation clobbers ini file when run with -p option

[txoof]

Describe the bug
The create documentation utility clobbers the paperpi.ini file when run with the -p option and wipes out all the other module configurations.

To Reproduce
Steps to reproduce the behavior:

1. run ./utilities/create_documentation.py -p foo_plugin
2. check ./config/paperpi.ini and see that all plugins other than foo_plugin are missing

Expected behavior
Should add foo_plugin to ini file without clobbering everything else