16bit workflow with hugin
This tutorial doesn't cover reasons why you might want to shoot with RAW and stitch in 16bit format. It is a simple HOWTO listing the tools available and how to use them with hugin.
Preparing the 16bit images
Start by using dcraw to read the RAW files and batch convert them into portable 16bit per channel PPM files. RAW pictures from my Nikon 8700 have a .nef extension, so the command looks something like this:
dcraw -v -w -4 dscn*.nef
convert -rotate 270 -gamma 2.2 dscn3088.ppm dscn3088.tif convert -rotate 270 -gamma 2.2 dscn3089.ppm dscn3089.tif ...
Note that I rotated them at the same time since these are portrait shots. Gamma correction is also applied at this stage since RAW data is generally linear and difficult to view without colour profile management (not yet supported by hugin).
You can now delete the intermediate PPM files.
Stitching with hugin
autopano-sift currently only supports 8bit per channel images, so if you want to use this tool then you need to create temporary 8bit versions of each image, generate control-points and then replace the images with the full version. Create the 8bit files by adding -depth 8 to the convert command-line above.
This TIFF file is in 16bit per channel RGBA format, which is not viewable in most image viewers or web-browsers, so there is an extra step to create final 8bit per channel images. So open the file in a 16bit aware image editor such as cinepaint or krita, tweak the levels by eye, retouch and save in an 8bit per channel format such as JPEG.