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The disadvantage of installing on SD is that you have to do it on every SD card that you use. The advantage is that you can remove the program easily.
Check create_device_install.sh in the hello-world-example (1.5) to see how to create an installation script for your own app to internal flash. (It would be 'polite' to also provide an uninstall-script I guess.)
Note that iRex tells that programs installed on the internal flash will/might(?) be removed when upgrading to a new firmware version.
The programs posted here for the DR typically installed on the SD-card (xournal being the exception to this).
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