Clean up windows when closing the database; various list editor improvements.

Stop Gap_Open from trying to exit if the user presses cancel when asked to
save contig changes.

Clean up old windows when closing the database.  This prevents crashes
caused by stale $io references in the old windows.

Raise the contig editor window before asking if changes should be saved.
Reduces the chance of the save changes dialogue from being obscured by
other windows.  Also makes it easier to see which contig editor is being
referred to.

List editor windows are now tracked using an array variable instead of
by creating unmapped child windows of the main window.  List editor toplevel
windows are now direct children of the main window, which allows the window
clean-up code to find them more easily.

Only bring up the extended reads list view for lists that have the appropriate
magic enabled.  Normal lists, along with the contigs and allcontigs lists,
get the standard list editor instead.

Prevent the pop-up menu from appearing in the extended read list view if the
user right clicks on an entry that is not a valid read identifier.

When outputting to another list from the extended reads list, properly filter
out entries that are not valid reads.

Fixed a couple of contig reference leaks in list_proc.tcl

Try to speed up saving long read lists when closing the list editor.



git-svn-id: https://staden.svn.sourceforge.net/svnroot/staden/staden/trunk@3210 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1