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

[Copilot]

Copilot's findings

• Files reviewed: 4/4 changed files
• Comments generated: 3

[mnriem]

Please address Copilot feedback

[nkgotcode]

Addressed the review feedback in nkgotcode/spec-kit@3196cbc.\n\nValidated locally:\n- uv sync --extra test\n- uv run pytest tests/extensions/test_extension_agent_context.py::TestAgentContextSelfHeal tests/extensions/test_extension_agent_context.py::TestExtensionConfigWriters -q\n- uv run pytest tests/integrations/test_integration_subcommand.py::TestIntegrationInstall::test_install_backfills_agent_context_extension_when_missing tests/integrations/test_integration_subcommand.py::TestIntegrationInstall::test_install_non_default_refreshes_init_options_version_only tests/integrations/test_integration_subcommand.py::TestIntegrationUpgrade::test_upgrade_non_default_refreshes_init_options_version_only -q\n- uv run specify --help

[Copilot]

Copilot's findings

• Files reviewed: 4/4 changed files
• Comments generated: 2

[Copilot]

Copilot's findings

• Files reviewed: 4/4 changed files
• Comments generated: 0 new

[nkgotcode]

Addressed the follow-up review notes in b6d77be: self-heal now skips when the bundled extension is unavailable, restores prior config on install failure, and remains side-effect free for help output.

Validated locally:

• uv run pytest tests/extensions/test_extension_agent_context.py::TestAgentContextSelfHeal tests/extensions/test_extension_agent_context.py::TestExtensionConfigWriters -q -> 14 passed
• uv run pytest tests/integrations/test_integration_subcommand.py::TestIntegrationInstall::test_install_backfills_agent_context_extension_when_missing tests/integrations/test_integration_subcommand.py::TestIntegrationInstall::test_install_non_default_refreshes_init_options_version_only tests/integrations/test_integration_subcommand.py::TestIntegrationUpgrade::test_upgrade_non_default_refreshes_init_options_version_only -q -> 3 passed
• uv run specify --help -> exit 0
• git diff --check origin/main...HEAD -> exit 0

[mnriem]

Closed by #2882

[mnriem]

Actually closed by #2885

[mnriem]

Thank you for working on this. In spite of another PR making it in before this one. Sometimes that happens and with the influx of so many issues and PRs this sometimes happens. Again thank you!