shell: remove clutter from shell's Makefile

Remove clutter that was put into centralized Makefile.includes.
Merge pull request #857 from Kijewski/shell-remove-clutter

shell: remove clutter from shell's Makefile
Use subfolders in bin dir

Creating all object files in one directory is bound to produce name
clashes. RIOT developers may take care to use unique file names, but
external packages surely don't.

With this change all the objects of a module (e.g. `shell`) will be
created in `bin/$(BOARD)/$(MODULE)`.

I compared the final linker command before and after the change. The
`.o` files (e.g. `startup.o`, `syscall.o` ...) are included in the same
order. Neglecting the changed path name where the `.o` files reside, the
linker command stays exactly the same.

A major problem could be third party boards, because the location of the
`startup.o` needs to the specified now in
`boards/$(BOARD)/Makefile.include`, e.g.
```Makefile
export UNDEF += $(BINDIR)msp430_common/startup.o
```