Ok. Since you have migrated to openHAB 2 (that’s a great move by the way 
), you should start using the new Eclipse Smart Home (ESH) Designer (think of it like the 2.x version of the older openHAB Designer).
The error that you are getting:
"The chosen directory is not a valid openHAB configuration directory. Please choose a different one"
is usually because the designer cannot find your personal openhab.cfg and the default openhab_default.cfg files (from the OH1 world and not really needed in the OH2 world) Link1 Link2
You could continue to use OH1 Designer by placing these 2 files (empty) in your config folder (this should fix the error) but I recommend to move to the ESH Designer (it has more syntax checks and supports more stuff):
To install the new, ESH Designer see here: http://docs.openhab.org/installation/designer.html
Try the ESH Designer and let me know if you have any problems
Note: Check also @rlkoshak 's great info here:
http://docs.openhab.org/tutorials/migration.html (primary reference)
&
Migration from OH 1.x to OH 2 Tutorial (secondary)