fix: self-heal agent-context extension

[nkgotcode]

Description

Moves the agent-context extension repair path out of integration helpers and into the top-level CLI project startup path. Older projects now restore the bundled extension on normal CLI invocation while integration commands only update the active context config.

Fixes #2881.

Testing

• uv run python -m pytest tests/test_agent_config_consistency.py -q
• uv run python -m pytest tests/extensions/test_extension_agent_context.py::TestExtensionEnabledGate tests/extensions/test_extension_agent_context.py::TestAgentContextSelfHeal tests/integrations/test_integration_subcommand.py::TestIntegrationInstall::test_install_backfills_agent_context_extension_when_missing tests/integrations/test_integration_subcommand.py::TestIntegrationSwitch::test_switch_backfills_agent_context_extension_when_missing tests/integrations/test_integration_subcommand.py::TestIntegrationUpgrade::test_upgrade_backfills_agent_context_extension_when_missing -q

[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?

[nkgotcode]

Moved this to the top-level CLI startup path in aac1f2c: non-init commands now call _self_heal_agent_context_extension(Path.cwd()), and integrations only update agent-context-config.yml.

Rebased onto current main; the branch is now mergeable. Validation passed:

• uv run python -m pytest tests/test_agent_config_consistency.py -q -> 28 passed
• uv run python -m pytest tests/extensions/test_extension_agent_context.py::TestExtensionEnabledGate tests/extensions/test_extension_agent_context.py::TestAgentContextSelfHeal tests/integrations/test_integration_subcommand.py::TestIntegrationInstall::test_install_backfills_agent_context_extension_when_missing tests/integrations/test_integration_subcommand.py::TestIntegrationSwitch::test_switch_backfills_agent_context_extension_when_missing tests/integrations/test_integration_subcommand.py::TestIntegrationUpgrade::test_upgrade_backfills_agent_context_extension_when_missing -q -> 9 passed
• git diff --check origin/main...HEAD -> exit 0