1) Except watchdog Install all the plugins during manual installation.
2) Dont use dbprefix
3) Copy the following folders from manual to zip:
ow_userfiles/plugins/notifications/
ow_userfiles/plugins/newsfeed/
ow_userfiles/plugins/mailbox/
ow_userfiles/plugins/friends/
(and also if they create any new folders)

ow_static/themes (with js files)
ow_static/plugins/newsfeed/* (with js files)
ow_static/plugins/mailbox/* (with js files)
(and also if they create any new folders)

ow_pluginfiles/notifications/
ow_pluginfiles/newsfeed/
ow_pluginfiles/mailbox/
ow_pluginfiles/friends/
(and also if they create any new folders)

4) Download the Update pack and the install pack and check the missing files (if any add it to the updater folder and make necessary changes in upgrade.php)

5) In 1.6.0 we have copied ow_pluginfiles/base/wurfl/persistence/ folder from manual only 1 file "ow_pluginfiles/base/wurfl/persistence/b/e/ec06e0c6b7972ffb0d022a64716aae" is not copied bcoz timestamp changes in every install in that file. Kindly check the same in next version