Date-tree related tidyups#124
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Having both isn't kosher. Given we started with the new-style format, use that.
If they're not already out-of-date, they will be soon.
We don't need to store the log output, move them out of the way.
OpenTree's cert can be a bit flappy.
So we can remove the space-normalisation, teach newick parser to deal with spaces when parsing ott names. There's plenty of other places that make this assumption, so can't remove the s/[_ ]/_/g yet, but this is worth doing for the future.
Break up into a separate parse_tree() / get_OTT_list().
It's seemingly not used anywhere, so don't save it.
Make enumerate_one_zoom_tokens know about the token_to_file_map, working out the relevant file name. Ideally it'd also manage the logic of which name/dist to use, but it's currently too complex. The resultant tree is identical.
To avoid proliferation of parameters, entertaining bugs when you get them the wrong way around, and to make it easier to include ot_required.
Pass the OT_required through to oz_tokens, so it can look for the orphan subtrees itself, and the copy step becomes unnecessary.
To avoid guesswork, match stages exactly to their executables
Downstream changes from previous commits
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A bunch of stuff from
issue-120-tree-splicerunrelated to the date work translated to DVC, and some DVC tidups.References #120