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.

[Copilot]

Pull request overview

This PR addresses issue #2881 by ensuring the bundled agent-context extension is backfilled (installed + registered) before integration flows update agent-context-config.yml, preventing projects from ending up with an inert config file and no runnable extension.

Changes:

• Add _ensure_agent_context_extension() to install the bundled agent-context extension when an integration has a context_file.
• Update integration init-options/config update flow to ensure the extension exists before touching its config.
• Add integration install/switch/upgrade tests that simulate missing agent-context and verify it is restored.

Show a summary per file

File	Description
src/specify_cli/integrations/_helpers.py	Ensures agent-context is installed before integration flows update its config.
tests/integrations/test_integration_subcommand.py	Adds regression tests asserting backfill behavior for install/switch/upgrade when agent-context is missing.

Copilot's findings

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• Files reviewed: 2/2 changed files
• Comments generated: 1

[mnriem]

The agent-context extension should self-heal at the extension-system level — not get backfilled by integration flows. Integrations are consumers of the config API, not owners of extension lifecycle.

How it should work:

1. agent-context auto-enables and self-heals at a top-level CLI hook (or during specify init)
2. Integration layer just writes to agent-context-config.yml, assumes the extension is there
3. Older projects get fixed on any CLI invocation, not only on integration install/switch/upgrade

Can you move the backfill logic out of _helpers.py and into the extension system instead?