chore: invoke migrated Jobs via the -i/-o short options

[tdudgeon]

Closes the Job Definition half of InformaticsMatters/squonk2-jobs#39.

What changed

Seven Jobs invoke scripts that now build their I/O options from
rdkit_utils.add_common_molecule_io_args(). Their command blocks moved from
--input/--output to -i/-o, and their Job Definition versions are
bumped per docs/versioning.md.

File	Job	Script	Version
rdkit.yaml	generate-low-energy-conformers	le_conformers.py	1.0.0 → 1.0.1
rdkit.yaml	rdkit-molprops	rdkit_props.py	1.0.0 → 1.0.1
rdkit.yaml	rdkit-dedup	rdkit_dedup.py	1.0.1 → 1.0.2
rdkit.yaml	sa-score	sa_score.py	1.0.0 → 1.0.1
rdkit.yaml	similarity-screen-rdkit	screen.py	1.0.0 → 1.0.1
rdkit.yaml	cluster-butina	cluster_butina.py	1.0.0 → 1.0.1
im-virtual-screening.yaml	enumerate-candidates	enumerate.py	1.0.0 → 1.0.1

Why the short forms, not --infile/--outfile

Issue #39 asked for the canonical long spellings. I tried that first and
jote failed 11 of 32 tests:

enumerate.py: error: the following arguments are required: -i/--input, -o/--output
rdkit_props.py: error: the following arguments are required: -i/--input

Every Job in this manifest pins tag: 'stable', and
informaticsmatters/vs-prep:stable was last published on 2024-06-10 — long
before the migration. It has no --infile/--outfile at all. So a definition
written with the long spellings cannot be loaded until a new image is published,
which turns a cosmetic change into a release-ordering problem.

-i and -o are canonical too, and they are the only spelling that works
against both the pre-migration image and the migrated code — and they survive
the eventual removal of the --input/--output aliases without a second pass.
They are also already how squonk2-desc-mordred, squonk2-desc-rdkit and
squonk2-train-test-split invoke their migrated scripts.

Verification

jote -m data-manager/manifest-im-virtual-screening.yaml, nextflow 22.10.0 to
match Dockerfile-nextflow:

• against the published vs-prep:stable — found=32 passed=32 failed=0
• against a locally built :latest carrying the migrated scripts, for the 7
  changed Jobs via --image-tag latest — found=11 passed=11 failed=0

The second run is the first time jote has exercised the migrated
virtual-screening scripts: the earlier post-migration run passed entirely on the
published 2024 image, so it validated the old code.

Deliberately unchanged

max_min_picker, le_conformers_for_mol, reactor, sucos, fail,
prepare_rdock, pharmacophore, convert_file, sdf_manip and the moldb
modules declare --input/--output themselves and never adopted the shared
group — renaming them would be a gratuitous breaking change. The
--input/--output on the two nextflow Jobs are params.input/params.output
for le_conformers.nf and enumerate.nf; both workflows already call their
scripts with -i/-o. cluster-butina's --output-fragment is its own flag.

Note that #39's scope table mislabels rdkit.yaml lines 1631–1632 as
cluster_butina.py; that command is python -m sdf_manip, which is out of
scope. The real scope was 7 Jobs, not 8.

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