refactoring to get pylint cleaner - some minor bug fixes in rarely used branches of code - Thanks, pylint
Removed #TODO comments - converted to issues on GH
Merge branch 'cleanup' into cleanup-refresh

I think that some order or merging PRs yesterday
left some of these commits off of master. It is just
pylint stuff, and I think that we looked them over already

I think that I had the merge of cleanup -> issue38 and
a separate PR of issue38 -> master. and we did them in the wrong
order. My fault. I should have noted the dependence in my PR
comment.

Conflicts:
	peyotl/__init__.py
	peyotl/api/wrapper.py
	peyotl/nexson_validation/_badgerfish_validation.py
	peyotl/nexson_validation/_by_id_validation.py
	peyotl/nexson_validation/_validation_base.py
	peyotl/nexson_validation/schema.py
	peyotl/phylesystem/__init__.py
	peyotl/string/__init__.py
	peyotl/test/test_phylesystem.py
	peyotl/test/test_string.py
	peyotl/test/test_treemachine.py
Reenabling a warning and added a pointer to docs

Old-style class warning used to be just pedantic, but
now that we support py3, we need to be warned (these
classes are no longer allowed).
Fixed py3 regression from my merge.

I'm still not used to making sure to convert
py3's dict key views to lists when I need
lists...
Merge pull request #63 from OpenTreeOfLife/cleanup-refresh

Cleanup refresh
Complicated Merge branch 'master' into ott

Handling PRs in the wrong order and splitting the
py3 and pylint branches off from master (rather
than in series) led to so serious headaches...
:-(

Conflicts:
	dev/pylintrc
	peyotl/api/__init__.py
	peyotl/api/oti.py
	peyotl/api/phylesystem_api.py
	peyotl/api/treemachine.py
	peyotl/api/wrapper.py
	peyotl/nexson_syntax/__init__.py
	peyotl/nexson_syntax/nexson2nexml.py
	peyotl/nexson_validation/_by_id_validation.py
	peyotl/nexson_validation/_validation_base.py
	peyotl/nexson_validation/err_generator.py
	peyotl/nexson_validation/helper.py
	peyotl/nexson_validation/logger.py
	peyotl/nexson_validation/schema.py
	peyotl/nexson_validation/warning_codes.py
	peyotl/ott/__init__.py
	peyotl/phylesystem/__init__.py
	peyotl/phylografter/nexson_workaround.py
	peyotl/phylografter/sync.py
	peyotl/string/__init__.py
	peyotl/test/support/pathmap.py
	peyotl/test/test_create_GitAction.py
	peyotl/test/test_oti.py
	peyotl/test/test_phylesystem_api.py
	peyotl/test/test_string.py
	peyotl/test/test_struct_diff.py
	peyotl/test/test_tmp_file_write.py
	peyotl/test/test_treemachine.py
	peyotl/test/test_v2facade.py
	peyotl/utility/__init__.py
	peyotl/utility/simple_file_lock.py
Merge branch 'ott' of github.com:OpenTreeOfLife/peyotl into ott