What, no solution?
ImageJ can run on Linux, and so does ALE.
The NetPBM tools can also do these things with two images (look at pnmarith, pnmcomp and ppmmix).
ImageMagick comes with a "composite" tool (and then why not use "compare" to check the improvements you obtain by merging?).
LibPano and Hugin can stitch images, and Enblend can make the composite more seamless.
All of the above, except Hugin, are in the Debian repositories.
See perhaps also
this message. PhotoAcute works in WINE.