ctx_build.c: uses getopt for cmd line args

ctx_build.c:
- now handles its own command line arguments with getopt

ctx_correct.c:
- add -c,--colour <C> option to specify which colour to correct against

Renaming files:
- graph_file_filter.c -> graph_file_reader.c
- path_file_filter.c -> path_file_reader.c

Renaming structs:
- AsyncIOReadTask -> AsyncIOReadInput