Q: In second question, suppose I have modified 'class.nav.php' and same
file got modified in the new version, how do we overcome this code
conflict issue other can manually comparing and applying my changes
again?A: You can either use github (and use it to merge your changes) or you would have to re-apply your changes manually with each upgrade. Or you could put your changes into a plugin. Q: If I modified an existing DB table by adding a column, same table is
modified in newer version, will my modification remain in the table if I
update to new version? A: this is really too broad of a question for me to actually answer. It would depend on the forth coming database changes that haven't happened yet, and what you did to the tables. I think that your best bet is to create your own tables to store what you want to store as the devs definitely wouldn't touch those since they won't even know about them. :)