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This also amends the test suite.
The git apply command to alter the stratum proved inflexible when
anything changed, so it has been replaced by a small in-line python
script.
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This reverts commit 2dc382a2a9ae977b1158002cd2631ec5593959c1, reversing
changes made to 89a019af088ff62459699a6efdadf8ac8fe35dd9.
We decided to restore the old commands for the release, as we weren't
confident the new implementations were correct yet.
To gain that confidence we need to use them, so the old versions are no
longer available, and the new edit code is used when the edit subcommand
is invoked.
Doing so also requires the test suite to use the edit command instead of
new-edit.
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The test suite got adapted so it requires the new edit instead of the
old one. So use the new edit instead of the old one in the test.
This is a kluge, and needs to be reverted after the BR10 release.
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I shouldn't be doing this in the middle of refactoring, but trying to
get the new code to emit exactly the right kind of JSON is too much pain,
and these tests need to be rewritten to use YAML in the near future anyway
(we'll drop JSON support eventually), so I don't want to spend more time
on this than necessary.
The changes in this commit convert morphologies in JSON to YAML, and
fix test code that modifies the morphologies to work with the YAML.
There is probably more JSON lurking about.
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This works sub-optimally, `morph edit $system $stratum` needs to be
done first as `morph edit $system $stratum $chunk` fails if $chunk
is not defined in the parent branch.
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