Revert "Makefile.in: corrected references to Makefile.dep (lives in SOURCE dir)"

This reverts commit a1000b301dffe5091d3719fc7fc834b2e3bca63a.
removed Makefile.dep from version control; build it in build directory
Makefile.in: remove generated Makefile.dep for `make clean`
Merge pull request #6 from insaneinside/build-system-fixes

Remove Makefile.dep from version control to avoid dependency-path issues