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So I have an idea of what I did wrong, I am just not sure how to fix it.

I used the Unity Glass mod:

After removing it, I cannot reset unity and it does not work.

Even after purging Unity and reinstalling it, I cannot seem to replace the missing files.

$unity --reset
WARNING: Unity currently default profile, so switching to metacity while resetting the  values
unity-panel-service: no process found
Checking if settings need to be migrated
Checking if internal files need to be migrated
Backend     : gconf
Integration : true
Profile     : unity
Adding plugins
Initializing core options...done
compiz (core) - Warn: failed to receive ConfigureNotify event on 0x1c00027

Initializing composite options...done
Initializing opengl options...done
Initializing decor options...done
Initializing vpswitch options...done
Initializing snap options...done
Initializing mousepoll options...done
Initializing resize options...done
Initializing place options...done
Initializing move options...done
Initializing wall options...done
Initializing grid options...done
I/O warning : failed to load external entity  "/home/arcline/.compiz/session/10b624e5c8f98c5325134625607758338300000051770001"
Initializing session options...done
Initializing gnomecompat options...done
Initializing animation options...done
Initializing fade options...done
Initializing unitymtgrabhandles options...done
Initializing workarounds options...done
Initializing scale options...done
compiz (expo) - Warn: failed to bind image to texture
Initializing expo options...done
Initializing ezoom options...done

(compiz:7038): Gtk-WARNING **: Theme parsing error: gnome-panel.css:28:11: Not using units is deprecated. Assuming 'px'.

(compiz:7038): GConf-CRITICAL **: gconf_client_add_dir: assertion `gconf_valid_key (dirname, NULL)' failed
Segmentation fault (core dumped)
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I have the same problem. unity --reset only takes me to"Initializing composite options...done", then nothing happens until I stop the process. – speter Sep 16 '12 at 22:36
The Segmentation fault (core dumped) message indicates a crash, so this should be reported as a bug. You can make Apport collect and submit the necessary technical information--but still make sure to read the bug reporting documentation first, and describe the problem thoroughly in the bug report you write in the web browser (which will come up automatically after Apport sends the data). – Eliah Kagan Sep 16 '12 at 22:42

It looks to me like your compiz settings need to be reset (manually). To do this, remove ~/.compiz-1, ~/.compiz and ~/.config/compiz or ~/.config/compiz (if they exist; depends on your compiz version).

Also, you can delete ~/.gconf/apps/compiz-1 to be safe.

So long as you have reinstalled Unity, this should fix it.

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Its always a really good idea to make a backup of a working compiz settings. You could export the settings in CompizCofig Manager. If something goes wrong you should first reset compiz settings there and after that import your working configuration an logout/login. After login you should have a working configuration again.

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