There are a number of cases where auto-indent isn't correct in Clojure. Here are some examples:

Instead of needing to delete all folders, then re-add. See http://www.sublimetext.com/forum/viewtopic.php?f=4&t=1524&sid=6f1d2c186c268381dfb2e4dc130aa5e5

As an eclipse user I really miss the Mylyn functionality (quick demo http://www.youtube.com/watch?v=IEyjpDrHCjc)

In my mind a basic task-focused interface would cover:
1. task creation/import - I can define local tasks and there's an API for writing connectors that retrieve tasks from remote issue trackers
2. every task carries it's own persistent context (primarily which files are open) and when I activate a task the context is restored

Basically make it more like Chrome and integrate the tabs and the title bar into one, to preserve pixels.

When auto completing a function pop up a small off-set message of the parameter inputs.
ex: foo( int a, real b ); // declared above
when foo auto-completed "foo(" is put and a message shows "foo( int, int )"

Allow the user to persistently change the font size independently for each pane in the UI. For example, the user should be able to use a smaller font size for the console pane than their main text buffer.

Currently, a series of files or folders which are numbered are not sorted correctly in the sidebar if they enter the hundreds. For example:

1
10
100
101
2

While I know this is often how *nix systems sort, I think many would agree that the intent of a series of numbered folders would be to sort correctly, as if they were integers.

Go to the python console and type "import ctypes" in build 2139 and you'll get:

>>> import ctypes
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File ".\ctypes\__init__.py", line 10, in <module>
ImportError: No module named _ctypes

Please add the ability to hide the scroll bar(s).