Pre configure not handling -S variables properly.

[wxtim]

Describe the bug

-S 'Variable="something"' doesn't get passed to the rose config loader in the pre_configure entry point, so all Cylc commands which rely on that entry point will not load it into the rose configuration.

This has not affected the cylc install workflow; cylc play workflow recipe because the contents of -S are stored in opt/rose-suite-cylc-install.conf.

Release version(s) and/or repository branch(es) affected?

Steps to reproduce the bug

With a blank rose-suite.conf and flow.cylc thus:

[scheduling]
    initial cycle point = 1066
    [[dependencies]]
        R1 = foo

[runtime]
    [[foo]]
        script = echo {{ GREETING }}

run

> cylc validate . -S 'GREETING="Hello"'
Jinja2Error: 'GREETING' is undefined
Context lines:
    [[root]]
        script = """
            echo {{ GREETING }}	<-- UndefinedError

Expected behavior

The test above should validate.

Additional context

• A quick inspection of the code of rose/metomi/rose/config_tree.ConfigTreeLoader.load suggests that -D and -S must be merged before being passed to load(). (Double check this)
• You will probably want to change the handling of opts.rose_template_variables at around line 240 of cylc-rose/cylc/rose/utilities.py

Pull requests welcome!
This is an Open Source project - please consider contributing a bug fix
yourself (please read CONTRIBUTING.md before starting any work though).

[oliver-sanders]

FYI: The origin of this bug was as a consequence of cylc/cylc-flow#4288, cylc/cylc-flow#4293

[wxtim]

Fixed by #132