I looked at the source code after considering everyone's comments.
After looking at the code I realize this isn't really a bug fix, it is
more of a behavior modification. Since this is the case, I thought I
would ask here before I make any changes.

I can modify the SpatialExecutorPlugIn to create a "normal" selection
if the user doesn't NOT choose to place the selection in a new layer,
but to clone features if they choose to put the selection in a new
layer. To do this I'll need to modify the constructor of the
SpatialQueryExecutor class to accept a boolean parameter indicating
the users choice. At this current time that boolean value is stored in
the SpatialQueryPlugIn class, and the SpatialQueryExecutor doesn't
have access to it. The SpatialQueryExecutor needs access to this
boolean parameter if it is to behave in the way I describe.

It won't take me long to make and test this change. A couple of hours
at the most.

I will move forward if we can agree that the plug-in behavior should
be modified as I describe.

SS

P.S. - Thanks goes to Stefan, Edgar, and Michael for helping me figure
this "bug" out. :]

On Mon, Mar 9, 2009 at 7:49 AM, Sunburned Surveyor
<sunburned.surve...@gmail.com> wrote:
> Thanks for the clarification Stefan and Michael. I now understand that
> it is only possible to "copy" features from the selection, and not to
> "cut" them, as I had thought. I will look at the code today on my
> lunch break to see what can be done about this.
>
> Landon
>
>
> On Mon, Mar 9, 2009 at 2:11 AM,  <edgar.sol...@web.de> wrote:
>>
>>> (1) in fact, I'm not sure if having the same feature in several layers
>>> (without clone) is a good or a dangerous idea. I think it could be nice
>>> to have a kind of "view" (like in database) to be able to work easily on
>>> a small part of a large featurecollection or to apply different styles
>>> to a featureCollection without cloning objects...
>>>
>>
>> This might confuse users, but also helps to save memory ... maybe enable
>> this as a choice for advanced users?
>> Of course every change in on layer changes all instances in every other
>> layer, but this may be on purpose.
>>
>> regards ede
>>
>>> Sunburned Surveyor a écrit :
>>>
>>>> Before I examined the source code for the spatial query bug, I decided
>>>> to see if I could duplicate the incorrect behavior.
>>>>
>>>> I was not able to do this.
>>>>
>>>> I successfully executed a spatial query and was able to copy & cut the
>>>> resulting selection from the source layer, pasting the selected
>>>> features to a destination layer.
>>>>
>>>> Has anyone else been able to duplicate this bug? As far as I can tell,
>>>> the selections created by the spatial query tool behave like all other
>>>> JUMP selections.
>>>>
>>>> If someone can confirm this isn't a real bug, I will close the bug
>>>> report. In this case, I will take a look at the other bug that Stefan
>>>> mentioned.
>>>>
>>>> The Sunburned Surveyor
>>>>
>>>> On Fri, Mar 6, 2009 at 2:51 PM, Sunburned Surveyor
>>>> <sunburned.surve...@gmail.com> wrote:
>>>>
>>>>
>>>>> I meant to say "check with you on the desired behavior of the plug-in"...
>>>>>
>>>>> SS
>>>>>
>>>>> On Fri, Mar 6, 2009 at 1:51 PM, Sunburned Surveyor
>>>>> <sunburned.surve...@gmail.com> wrote:
>>>>>
>>>>>
>>>>>> Thanks for the help Stefan. I hope to start work on this bug next
>>>>>> week. I may need to check on the desired behavior of the plug-in again
>>>>>> after I have looked at the code.
>>>>>>
>>>>>> SS
>>>>>>
>>>>>> On Fri, Mar 6, 2009 at 12:09 PM, Stefan Steiniger <sst...@geo.uzh.ch> 
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>>> Hei,
>>>>>>>
>>>>>>> so I just had to check... it is the plugin:
>>>>>>> ui.plugin.analysis.SpatialQueryPlugIn of the original JUMP
>>>>>>>
>>>>>>> the case where the selection is needed is for instance if feature in one
>>>>>>> layer appear also in a second layer and one wants to find those using
>>>>>>> "equal".
>>>>>>> Then the goal would be to delete or modify the features that appear in 
>>>>>>> both
>>>>>>> layers (e.g. "cut selected items" doesn't work) - I attach two datasets.
>>>>>>>
>>>>>>> stefan
>>>>>>>
>>>>>>> Sunburned Surveyor wrote:
>>>>>>>
>>>>>>>
>>>>>>>> Here is the link to the bug tracker page for the bug I am talking 
>>>>>>>> about:
>>>>>>>>
>>>>>>>>
>>>>>>>> http://sourceforge.net/tracker/index.php?func=detail&aid=2660272&group_id=118054&atid=679906
>>>>>>>>
>>>>>>>> SS
>>>>>>>>
>>>>>>>> On Fri, Mar 6, 2009 at 11:08 AM, Sunburned Surveyor
>>>>>>>> <sunburned.surve...@gmail.com> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>> I will start work on squishing the bug that has to do with "phantom"
>>>>>>>>> feature selections produced by the spatial query functionality in
>>>>>>>>> OpenJUMP.
>>>>>>>>>
>>>>>>>>> Can anyone tell me if the spatial query functionality is part of the
>>>>>>>>> core program, or part of a plug-in? That will help me track down the
>>>>>>>>> source code so I can get started.
>>>>>>>>>
>>>>>>>>> SS
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
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>>>>>>> -Strategies to boost innovation and cut costs with open source 
>>>>>>> participation
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>>>> CA
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>>>> -Strategies to boost innovation and cut costs with open source 
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>>>
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>>> -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
>>> -Strategies to boost innovation and cut costs with open source participation
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>> -Strategies to boost innovation and cut costs with open source participation
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