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Reading of this book http://shop.oreilly.com/product/9780596002220.do is strongly recommended. Practically speaking, that book covers all the issues involved in developing software for such systems (from tool chain organization to the most famous file systems running on top of MTD). It is not a reference guide, but it provides a complete and exhaustive overview that makes the developer to save a lot of time in searching such information over the Internet.
===Links===
If you need a brief but still exhaustive overview of the Linux and Embedded Linux world, please have a look at the excellent training section of Free Electrons web site: http://www.free-electrons.com/docs/.
Another rich source of information is the web site http://elinux.org.
This [http://140.116.72.245/~q36991217/allenli/wp-content/uploads/omap/TTO_Linux_SOC_Workshop_Student_Notes_v3.08.pdf link] points to a document writtend by Texas Instruments for a student workshop. Even if it addresses Texas Instruments processors, it provides a lot of useful information that are platform-independent.