Moved cmd.c -> src/basic/cmd.c; Split out src/kmer/cmd_mem.c

1. split cmd_mem.c (out of cmd.c) to handle memory calculations
2. moved src/kmer/cmd.c -> src/basic/cmd.c
3. added cmd_get_cmdline(), cmd_get_cwd() to cmd.h
4. clean_graph.c: print number of nodes removed by tips/supernodes/both