pack: add $namespaces to the (effective) root only

[mr-c]

As per schema-salad, $namespaces are only valid in the root document:

https://www.commonwl.org/v1.0/SchemaSalad.html#Explicit_context
https://www.commonwl.org/v1.1/SchemaSalad.html#Explicit_context (same as v1.0)
https://www.commonwl.org/v1.2/SchemaSalad.html#Explicit_context (same as v1.0, v1.1)

Inspired by (and partial fix for) common-workflow-language/cwl-utils#71 (comment)

[codecov]

Codecov Report

Merging #1506 (62e3d40) into main (5a1488b) will decrease coverage by 0.04%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main    #1506      +/-   ##
==========================================
- Coverage   65.67%   65.63%   -0.05%     
==========================================
  Files          89       89              
  Lines       15902    15906       +4     
  Branches     4027     4029       +2     
==========================================
- Hits        10444    10440       -4     
- Misses       4329     4337       +8     
  Partials     1129     1129              

Impacted Files	Coverage Δ
cwltool/pack.py	86.74% <100.00%> (+0.14%)	⬆️
job.py	61.49% <0.00%> (-0.81%)	⬇️
cwltool/job.py	77.66% <0.00%> (-0.41%)	⬇️
pack.py	9.39% <0.00%> (-0.11%)	⬇️

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[simleo]

If anyone has an old packed workflow that you can't read with cwl-utils due to this, here's a workaround:

import json
from pathlib import Path
from cwl_utils.parser import load_document_by_yaml

wf_path = Path("packed.cwl")
with open(wf_path, "rt") as f:
    json_wf = json.load(f)
graph = json_wf.get("$graph", [json_wf])  # support single tool
for n in graph:
    ns = n.pop("$namespaces", {})
    if ns:
        json_wf.setdefault("$namespaces", {}).update(ns)
doc = load_document_by_yaml(json_wf, wf_path.absolute().as_uri())