I have noticed a bit of weirdness related to this as well.  There are
two main issues that I have seen in this dialog:

1)  The logic to determine when a layer needs uploading seems to mark
it as requiring upload very frequently, but then if you cancel out of
the dialog and press the upload button manually, it says there are no
changes to upload (which is actually correct), so the two systems both
seem to have their own logic, with the one in the exit dialog not
being as robust as the one on the normal upload button.  Re-using the
code from the upload button should make the codebase smaller, and
would probably fix many of the issues outlined in the previous
message.

2)  A possible cause of your duplicated objects from the upload can be
the result of something I filed a trac ticket about a while back,
namely that after you do an upload to a layer that exists on the hard
disk, it would be nice to have an option to automatically save the
file to disk after the upload happens so that object ID's on new
objects get written to disk immediately.  More than once (in fact just
the other day) I have uploaded something and forgot to save afterward
and then after re-opening josm at a later time and doing more work in
the area, some objects get uploaded a second time since the file was
not saved to disk after the previous successful upload.  Putting the
"save to disk after upload" option in the upload window on the tab
with the "leave changeset open" checkbox seems like a natural place to
put it.  Obviously this only applies to layers which actually exist on
disk, if someone just downloads, edits, and uploads without ever
saving then the state of this new checkbox can just be ignored on
upload.

Here is the trac ticket mentioned in point #2:
http://josm.openstreetmap.de/ticket/7487

Regarding the points made about setting flags on layers, I think this
is a good idea and would like to see more of these kinds of
protections.  We currently have upload=false and the previous poster
mentioned a couple more that could work similarly.  Knowing the source
of the data in a layer and how that should be combined with other
layers and/or uploaded would make things a lot easier and less error
prone for people working with multiple data sources.

-AndrewBuck

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