Write inline test jobs outside source directories

[jmchilton]

Supersedes #1438.

Motivation

When a workflow test embeds its job definition directly in the test YAML, Planemo currently serializes that job to a temporary JSON file beside the test definition. This briefly modifies the source checkout and requires the source directory to be writable.

#1438 correctly proposed moving these generated files to the system temporary directory. However, the location of a job file is also the base directory for relative test-data paths, so moving the file without preserving that base breaks inputs such as path: hello.txt.

Changes

• Materialize inline test jobs in a dedicated system temporary directory instead of the workflow or code directory.
• Resolve local File and Directory paths against the original test-definition directory before serialization.
• Preserve relative-path behavior for nested collections, secondary files, and composite inputs.
• Leave remote URIs, unrelated path parameters, and the original in-memory test definition unchanged.
• Clean up the complete temporary directory on success and on exceptions.

Validation

• Added focused regression coverage for temporary-file placement, nested relative inputs, URI preservation, immutability, and exception cleanup.
• Passed 16 focused and adjacent engine tests.
• Passed test_galaxy_workflow_nested_collection_inputs against a real managed Galaxy, exercising nested collections whose inputs use relative hello.txt paths.
• Passed Black, isort, flake8, and git diff --check for the changed files.