Some points based on my recent attempts:
- Instead of re-inventing the wheel, you can check if the particular package already exists in the debian armel wheezy or jessie repositories. If yes, they can be directly copied to the kindle and most will run. You need to copy any library dependencies too.
- As indicated in the link given by encol, you can set up a debian armel VM and compile and test stuff on it and later copy it over to the kindle.
- You can also do a cross compile from a desktop linux. This seems to produce executables that are better in terms of speed.
- All the above is for command line applications. For graphical applications, you need to fiddle further with things like GTK. (I haven't got there yet! ;-))
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