Convert ctx_join and ctx_subgraph to using getopt_long()

cmd.c: add cmd_check() to print error if option given twice
Don't track Object file
ctx_reads.c: uses getopt_long()

async_read_io.c: collected common async IO from:
- correct_reads.c
- generate_paths.c
- build_graph.c

async_read_io.c: AsyncIOReadInput -> AsyncIOInput