[Makefile] add dependencies

Before
=====
```
$ make -B libneko
~~ snip ~~
$
$ touch vm/neko_mod.h   # (edit vm/neko_mod.h)  || (update by git pull/checkout)
$ make libneko
make: Nothing to be done for 'libneko'.
$ ???
```

After
====
```
$ make -B libneko
~~ snip ~~
$
$ touch vm/neko_mod.h
$ make libneko
~~ snip ~~   # rebuild
$ :)
```

dependency file is auto generated by `make dep`.