fix: backfill agent-context extension for integrations

[nkgotcode]

Description

Backfills the bundled agent-context extension before integration install, switch, and upgrade flows write agent-context-config.yml. This keeps recovered or older projects from ending up with only the config file and no runnable agent-context extension files.

Fixes #2881.

Testing

• Tested locally with uv run specify --help
• Ran existing tests with uv run python -m pytest tests/integrations/test_integration_subcommand.py tests/extensions/test_extension_agent_context.py tests/test_agent_config_consistency.py -q
• Tested with a sample project: initialized Copilot, removed .specify/extensions/agent-context plus its registry entry, then ran specify integration upgrade copilot --script sh --force and verified the extension files and config were restored.

Validation output:

uv run specify --help
Usage: specify [OPTIONS] COMMAND [ARGS]...
Commands: init, check, version, self, extension, preset, integration, workflow

uv run python -m pytest tests/integrations/test_integration_subcommand.py tests/extensions/test_extension_agent_context.py tests/test_agent_config_consistency.py -q
128 passed in 12.62s

sample backfill OK: .github/copilot-instructions.md

AI Disclosure

• I did use AI assistance (describe below)

This fix was prepared and validated with AI-assisted coding-agent support under human-operated OSS factory workflow controls.