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I haven't seen any problem with the modified popupmenu, and I was using your version until yesterday.
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That's very interesting to know. For me, the "menu screw up" problem happens most times, after disconnecting from the PC. Maybe it is a Windows problem? :-)
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Try the packaged attached.
Copy "ctb" and "popupmenu" programs to "/usr/bin/", the .png images from the 2 directories (without the directories) to "/usr/share/icons/" and "ctb.rc" to "/usr/share/ctb/", then reboot the device.
Obviously you need DR1000 uds binary installed on "/usr/bin/" as well.
It's working smoothly on my DR800S.
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I don't have the reader at hand now, but I tried on the emulator, looks great! Although I might like some more icons on the status bar, such as "select zoom" and "annotation". But that's just personal preference. I believe you are going to post the source when you release it?
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And now the one-million dollar question:
I think the programs are ready to be announced and used for the general public, but I don't think I can include IREX DR1000 uds binary here due to its copyright, as is not GPL. Thus it's not possible to create a complete and easy to install package for normal users.
What do you think?
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The only thing needed for Windows is some tool to extract the rootfs.bin file. I have searched on the internet when I did the change, but no luck. On Linux, this is so easy. But if someone uses Linux, I don't think he/she needs this "one-step" setup program.