Fix module-level dict mutation in galaxy-config-init

[Copilot]

PR galaxyproject#21049 introduced a bug where main() mutates the module-level GALAXY_CONFIG_SUBSTITUTIONS dictionary when --db-conn is provided, causing side effects across function calls.

Changes

• Create local copy of GALAXY_CONFIG_SUBSTITUTIONS before modification
• Pass substitutions dict as parameter to _handle_galaxy_yml()
• Use local copy instead of module constant

# Before
def main(argv=None):
    # ...
    if args.db_conn:
        GALAXY_CONFIG_SUBSTITUTIONS["  #database_connection: null"] = "..."  # Mutates module state
    _handle_galaxy_yml(args, config_dir, data_dir)

# After  
def main(argv=None):
    # ...
    substitutions = GALAXY_CONFIG_SUBSTITUTIONS.copy()
    if args.db_conn:
        substitutions["  #database_connection: null"] = "..."  # Modifies local copy
    _handle_galaxy_yml(args, config_dir, data_dir, substitutions)

Fixes architectural issue while preserving functionality.

Original prompt

PR https://github.com/galaxyproject/galaxy/pull/21049/files in the upstream repository is wrong. The fix is in this comment usegalaxy-eu/infrastructure-playbook#1693.

Create a branch in kysrpex/galaxyproject-galaxy that fixes the issue. I will open a PR manually using that branch later in galaxyproject/galaxy.

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