Fix shared script command hints for integration separators

[WOLIKIMCHENG]

Summary

• Render bundled shared script command hints with the active integration invoke separator
• Refresh managed shared infrastructure when default integration state/options change
• Add regression coverage for dot and hyphen refs across bash, PowerShell, switch/use/upgrade paths, and customized shared script preservation

Fixes #2587.

Testing

• uv run python -m pytest tests/integrations/test_cli.py::TestSharedInfraCommandRefs -q
• uv run python -m pytest tests/integrations/test_integration_subcommand.py::TestIntegrationUpgrade::test_upgrade_default_refreshes_shared_script_refs_for_option_separator_change -q
• uv run python -m pytest tests/integrations/test_integration_subcommand.py -q
• uv run python -m pytest tests/integrations/test_integration_base_skills.py tests/integrations/test_integration_copilot.py -q
• uv run python -m pytest tests/test_agent_config_consistency.py -q
• uv run specify --help
• Manual temp-project checks for Claude sh/ps, Copilot sh, and Copilot upgrade to --skills with customized shared script preservation