Hola Leonardo,
Very nice to have you here, welcome.
About your changes of some of the input fields to support the rich text editor, If you could send me the example "http://www.xmlportletfactory.org/1-table-2-fields-varchar-and-text" with your changes, I would try to insert them as part of the "standard". Your contribution is very welcome.
About the re-generating / overwrite, probably you would do just remarking the corresponding application.
Use <!-- before <application> tag and --> after </application> tag. This way it wont generate code for it, but wont erase previous generated code, will keep JSPs and .javas, but will overwrite language.properties.
Dont forget to get back to comment your results.

Saludos, Jack.