Finished BreakpointCaller
Renamed `ctx31 call` command to `ctx31 bubbles`
Add --min_ref and --max_ref arguments to ctx_breakpoints

0. ctx_breakpoints.c:
* Add --min_ref and --max_ref arguments to ctx_breakpoints to specify required
  homology with the reference to declare a breakpoint
* Add check to see if output file already exists

Convenience MACROs:
1. file_util.h: futil_outpath_str(path), futil_inpath_str(path) return path or
                "STDOUT"/"STDIN" if path is "-"
2. util.h: util_plural_str(n) return "s" if != 0, "" otherwise
BreakpointCaller: flank5p is treated like alleles

ctx_breakpoints.c: fixed memory calculation to include ref annotation
Cosmetic changes
Fix total colours count in ctx_clean
Second attempt at fixing ncols counting bug
Fix BUG causing `ctx thread` to ignore -p arg; Fix small memory leaks

ctx_thread.c:
* BUG FIX: load paths for the colour being used annotated
* ctx thread was effectively ignoring -p argument

path_format.c:
* added path_load_colour() function similar to graph_reader.c:graph_load_colour()

merged FileFilter dealloc()/close() methods
* file_filter_dealloc() -> file_filter_close()
* graph_file_dealloc() -> graph_file_close()
* path_file_dealloc() -> path_file_close()
* fixes several small memory leaks in ctx commands

graph_crawler.c
* unicol_path_cmp() now compares empty paths correctly
Subgraph can grab entire supernodes; Bug fixes for breakpoint_caller

Note: There are still outstanding bugs in the breakpoint caller

ctx_subgraph.c:
1. fixed bug causing total_cols to always be set to zero
2. changed command line usage for ctx_subgraph.c:
   - requires --dist <D> instead of taking <dist> <in.ctx>
   - added --supernodes to pull out entire supernodes touched by a read

subgraph.c:
0. renamed struct EdgeNodes -> SubgraphBuilder
1. added grab_supernodes option to pull out entire supernodes touched by a read
2. added tests for above feature in src/tests/subgraph_tests.c

kmer_occur.c:
1. Fixed BUG: split ref sequences at Ns when loading
2. Fixed BUG: array resizing bug in kmer_occur that was causing an out-of-bounds
              warning from valgrind

graph_crawler_tests.c:
1. Added tests which identified and fixed bugs in:
   - graph_cache.c
   - graph_crawler.c

breakpoint_caller.c:
1. fixed BUG: next_nodes incorrect indexing due to removing next nodes that are
              in the ref
Breakpoint Caller fixed: Fix GraphWalker counter path crash with Breakpoint Caller