Fix job_config_init profile wiring and legacy version default

[jmchilton]

Two independent bugs in job_config_init / profile_job_config_init, both found while addressing review comments on #1683.

profile_job_config_init records the wrong file

initialize_job_config writes job_conf.yml into the profile directory and then stores the profile's own planemo_profile_options.json path as job_config_file:

config["job_config_file"] = os.path.abspath(profile_config_path)

A profile set up this way hands Galaxy its options JSON as a job configuration, so the generated runner configuration never takes effect. Before:

$ planemo profile_create slurm_cluster
$ planemo profile_job_config_init slurm_cluster --runner slurm
$ jq -r .job_config_file ~/.planemo/profiles/slurm_cluster/planemo_profile_options.json
.../profiles/slurm_cluster/planemo_profile_options.json

tests/test_cmd_profile_job_config_init.py only asserted exit codes, which is why this survived. It now asserts the recorded path and parses the config it points at.

--galaxy_version defaults to the legacy layout

galaxy_version_option() pins the click default to "24.2", while gxjobconfinit defaults to "25.0" when the value is None and branches on galaxy_version < "25.0". Omitting the flag therefore selects the legacy configuration rather than a modern one.

For --runner slurm --singularity the output is byte-identical either way. For --tpv it is not:

	with --galaxy_version 25.0	default (24.2)
runner	dynamic_tpv	dynamic + type: python + rules_module: tpv.rules
TPV config	inline tpv_configs	external tpv.yml the user must create
tpvdb_slurm destination	generated	commented-out template only

Passing None through lets the library's default apply and move with it. Callers that want the old layout still pass --galaxy_version 24.2 explicitly, which the existing test_job_config_init_24_2 covers.

Validation

• pytest tests/test_cmd_job_config_init.py tests/test_cmd_profile_job_config_init.py — 8 passed; both new tests confirmed red before the fixes
• flake8, black --check, isort --check-only clean on all changed files
• docs/commands/{job_config_init,profile_job_config_init}.rst regenerated with scripts/commands_to_rst.py. The generator also rewrites eleven unrelated command docs that have drifted from merged PRs; those are left alone here.
• End-to-end: profile_create + profile_job_config_init --runner slurm --tpv --singularity now yields dynamic_tpv, an uncommented tpvdb_slurm destination, https://gxy.io/tpv/db.yml, singularity_cmd: singularity, a commented drmaa_library_path, native_specification, tmp_dir: true, and a profile recording the real job_conf.yml.

Relationship to #1683

#1683 drops --galaxy_version 25.0 from its examples and recommends profile_job_config_init, per review there. Both of those are only correct once this lands, so this should merge first.

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