Which directory in my plugin repo does WordPress Plugin Directory package?

you have to commit the changes to the /trunk directory yourself, changing the version number in the /trunk/readme.txt is not going to do this on its own.

Update

Whenever i update a version say from 1.0.0 to 2.0.0 i first create a directory in /tags
and name it just like the last version 1.0.0
the i copy everything from /trunk to it so if someone wants an older version he can get it.
the i just commit any changes of the new version to /trunk

so basically trunk holds only the latest version (no need to create a new directory in trunk.)