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This patch uses the same hacks listed in the "[PATCHES] Fixes for java
apps and firefox in scale, switcher and wobbly" message to apply the
transparency to the right windows; I don't think it will be merged,
but I'm posting it here just as example for other users/packagers;
however it can be disabled only setting the default opacity_values
value to 100...

Regards,
Treviño

- --
Treviño's Blog - Life and Linux
http://3v1n0.tuxfamily.org/blog/
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diff --git a/metadata/core.xml.in b/metadata/core.xml.in
index 8424ab1..1ccd795 100644
--- a/metadata/core.xml.in
+++ b/metadata/core.xml.in
@@ -449,11 +449,17 @@
 		<_short>Opacity windows</_short>
 		<_long>Windows that should be translucent by default</_long>
 		<type>match</type>
+		<default>
+		    <value>((type=Unknown | Menu | PopupMenu | DropdownMenu | Tooltip | Notification | Combo | Dnd | name=sun-awt-X11-XWindowPeer) | (type=Normal &amp; override_redirect=1)) &amp; !(name=sun-awt-X11-XFramePeer | name=sun-awt-X11-XDialogPeer)</value>
+		</default>
 	    </option>
 	    <option name="opacity_values" type="list">
 		<_short>Opacity window values</_short>
 		<_long>Opacity values for windows that should be translucent by default</_long>
 		<type>int</type>
+		<default>
+		   <value>89</value>
+		</default>
 	    </option>
 	</screen>
     </core>

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