Explicitly set $TOSROOT in the app Makefile

This removes the non-desireable requirement that a user must set
environment variables in order to build TinyOS. The $TOSROOT variable
then trickles through the makefiles and in makerules $TOSDIR is set.

The overhead to do this is small (1 line in each application makefile)
but it should really help make tinyos more user friendly.

TOSROOT is set with "?=" meaning that it won't override TOSROOT if it is
already set by an environment variable.

Makefile.include in the root sets TOSDIR and MAKERULES before including
$(MAKERULES). This allows the current env variables to override the
derived settings.
Updating documentation

No longer refers to environment variables. Also removed the upgrade
guide. Hopefully no one needs that any longer.
Cleaned whitespace
Moved python code to tools/, now gets installed

In order to remove more environment variable usage, the tinyos python
code must be installed on the user's system instead of in the tinyos
tree. This commit moves all the python to tools so automake will install
it. Doing this requires one subtle change: "import tos" will no longer
work. It needs to be "from tinyos import tos" now.

I think I updated all of the relevant files.

One note: python3 is handled a bit weirdly, and therefore tos-serlook.py
may not be able to find tinyos.misc.hexdump. It seems that
/usr/local/lib/python3/dist-packages is not in the search path by
default. I fixed this by adding "tinyos.pth" containing the correct
directory to /usr/local/lib/python3.2/dist-packages.
Removing references to the environment variables
Moved CoAP to /tools dir

The CoAP support code will now be built and installed with tinyos-tools.

I updated coap.extra to reflect the moved .c files.
Moved blip support to tools directory

Will not compile the blip sdk code on cygwin as it only supports linux and mac.
Moved sf and serial_tun to tools

I have no idea if anyone still uses this code. The configure script for
sf is out of date and does not work with newer automake (I updated it).

I also renamed some binaries so they can be installed. If the user is
installing TinyOS, they may as well _install_ tinyos. Why make them hunt
around for different binaries? If something shouldn't be installed, then
the question is why is it distributed with the main TinyOS source? It
should be some sort of optional extra somewhere, not part of the main
source. Hard drives are big, just give me all of the TinyOS tools.
Moved cpp version of sf to tools

Because there are 2 sf applications, the cpp version is named sf2.
Removed env vars from java sdk

Still would like to have this installed with the tools, but I'm working
on that.
Moved java to tools

Successfully compiles and creates the tinyos.jar file. I still can't
figure out how to install it, however. Java is annoying.