enh: update FILMGLS to support FSL release 5.0.5
enh: allow a single mask for fixed image
fix: allow contrast file to be an input and therefore hashed when content changes
enh: allow a depth first topological sort. in this scenario each isolated subgraph gets a topological sort ordering.
enh: allow hashing of parameterization to be controlled using a configuration option.
enh: removed old reporting - wip to replace with d3 based visualization
fix: handle edge cases of subgraphing of directed graphs
fix: freesurfer resume does not set any inputs
fix: resolve role as a resource with a uri
fix: make write provenance return a graph and add niiri as default namespace
tst: fix filmgls test
doc: update CHANGES
fix: add d3 to repo
fix: remove dummy run interface from recon-all
fix: resolved conflict
doc: rst syntax fix in joinnode doc
Merge remote-tracking branch 'upstream/master' into fix/reporting

* upstream/master:
  output_name example
  name_source for lists
  Added support for custom output names
  changelog
  Further cleanup
  All tests pass
  further cleanup
  begin aFNI refactor
sty: white spaces
Merge pull request #697 from satra/fix/reporting

WIP: Multiple fixes