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

[Copilot]

Pull request overview

This PR fixes a command-hint mismatch in bundled shared scripts by templating /speckit command references and rendering them with the active integration’s invoke_separator during shared infrastructure installation/refresh, ensuring hints match actual command invocations for both dot (/speckit.plan) and hyphen (/speckit-plan) styles.

Changes:

• Replaced hardcoded /speckit.* / /speckit-* references in shared bash/PowerShell scripts with __SPECKIT_COMMAND_<NAME>__ placeholders.
• Updated shared infrastructure installation to resolve __SPECKIT_COMMAND_*__ placeholders in shared scripts (in addition to templates) using the active invoke_separator.
• Expanded regression tests to cover script hint rendering and refresh behavior across install/use/switch/upgrade flows and customization preservation.

Show a summary per file

File	Description
src/specify_cli/shared_infra.py	Resolves __SPECKIT_COMMAND_*__ placeholders when copying shared scripts so command hints match the active integration separator.
src/specify_cli/__init__.py	Switches default/upgrade refresh paths to re-install shared infra (scripts + templates) with refresh_managed=True and updates related CLI/help messaging.
scripts/bash/check-prerequisites.sh	Replaces hardcoded /speckit.* hints with __SPECKIT_COMMAND_*__ placeholders for template-time rendering.
scripts/bash/common.sh	Updates comments referencing commands to use __SPECKIT_COMMAND_*__ placeholders.
scripts/bash/setup-tasks.sh	Replaces hardcoded /speckit.* hints with __SPECKIT_COMMAND_*__ placeholders.
scripts/powershell/check-prerequisites.ps1	Replaces hardcoded /speckit.* hints with __SPECKIT_COMMAND_*__ placeholders.
scripts/powershell/common.ps1	Updates comments referencing commands to use __SPECKIT_COMMAND_*__ placeholders.
scripts/powershell/setup-tasks.ps1	Replaces hardcoded /speckit.* hints with __SPECKIT_COMMAND_*__ placeholders.
tests/integrations/test_cli.py	Adds direct coverage ensuring _install_shared_infra renders shared script command refs for both dot/hyphen separators.
tests/integrations/test_integration_subcommand.py	Adds end-to-end regression coverage for script ref refresh across install/uninstall/use/switch/upgrade flows and customization preservation.

Copilot's findings

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• Files reviewed: 10/10 changed files
• Comments generated: 1

[WOLIKIMCHENG]

Addressed. integration use now passes a caller-specific shared infra refresh hint through _set_default_integration, so preserved/skipped shared files point users to specify integration use <key> --force. Added coverage to the existing integration-use preservation test.

[Copilot]

Copilot's findings

• Files reviewed: 10/10 changed files
• Comments generated: 2

[Copilot]

Copilot's findings

• Files reviewed: 10/10 changed files
• Comments generated: 0 new

[mnriem]

Please resolve conflicts

[WOLIKIMCHENG]

Hi @mnriem, I rebased the branch onto the latest main and resolved the conflicts. Thank you!