Most of this is personal preference for me, so I would take what I'm saying with a grain of salt.

There are some spacing issues here and there - the username/settings drop down next to the search input is not vertically aligned with the rest of the elements. The create new directory form and add URL form is pushed to the right a bit. I'd either center those or keep them aligned left.

One thing I'd try is making the create new directory part into a pop over. It would actually increase the time to create a new directory (additional click/tab), but in my case it'd be okay since I would be creating new ones so infrequently. The idea is a "new directory" button with that form in a pop over when active.

I'd consider using list elements instead of a table for the directory listing and link listing.

For the directory listing, I'd experiment with replacing the links count/action dropdown with something right next to or immediately below the link to the directory. i.e.

    MyDirectory <link icon> 3 • rename • remove

With more emphasis (using styles) on the name of the directory. Hovering over <link icon> 3 could have a title attr that said something like "3 links in MyDirectory".

But the project works fine and the UI isn't really taking too much away from using it.