Functionalizer

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Changes:
- Improved the determination of fields to write to the output

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Changes:
- Warn if entries in the classification matrix don't cover values. Also
adds option ``--strict`` to abort execution if any warnings are issued.
See FUNCZ-86_.
- Use MorphIO/MorphoKit to read in morphologies. See FUNCZ-199_.
- Add additional output columns to gap-junction runs. See FUNCZ-211_.
- Fix executions for circuits with only one synapse class. See FUNCZ-218_.
- Add preliminary SONATA support. See FUNCZ-217_.
- Add support for ``{from,to}BranchType`` in `TouchRules`. See FUNCZ-223_.

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Changes:
- Warn when synapse classification does not cover all values. See
FUNCZ-209_.

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Changes:
- Display intermittent touch count after checkpoints. See also
FUNCZ-201_.

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Changes:
- Add the fractional position along sections to the output.

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Changes:
- Allow touch rules to filter for more than soma, !soma. The following
values are valid in the `TouchRule` XML nodes (for the attribute
`type`):

- `*` accepts everything
- `soma` matches soma branches (type 0)
- `dendrite` matches everything that is not a soma (this reproduces the
old behavior. Since TouchDetector does not consider touches towards
axons in normal operation, this matches dendrites only normally)
- `basal` matches branches of type 2 (basal dendrites)
- `apical` matches branches of type 3 (apical dendrites)

Note that the notations correspond to the convention used for
morphologies saved as H5.
- Output touch positions: contour for efferent, center position for
afferent side.
- Output section type for the afferent side of touches.
- Output spine length
- Compare statistical properties of the resulting circuits in the CI
- Added a `--debug` command line flag to produce additional output