[bug-fix] Fix init-force-preset-desync: reapply presets/extensions on init --here --force

[github-actions]

Bug fix — init-force-preset-desync

Proposed fix for issue #3990, applying the remediation from the bug assessment.

Verdict: Valid · Severity: high

Summary

After specify init --here --force regenerated integration files from bundled core templates, installed presets were not recomposed, causing the on-disk files to silently revert to the pure core version while the preset registry still reported them as installed. This fix adds a call to _register_presets_for_agent and _register_extensions_for_agent after manifest.save() when force=True, mirroring the pattern already present in the integration upgrade path.

Changes

File	Change	Notes
src/specify_cli/commands/init.py	modified	Added _register_presets_for_agent + _register_extensions_for_agent call after manifest.save(), guarded on force=True
tests/integrations/test_cli.py	modified	Added two regression tests: one verifying the functions are called on init --here --force, one verifying they are not called on a fresh init without --force

Tests Added or Updated

• TestInitIntegrationFlag::test_init_here_force_reapplies_installed_presets — verifies _register_presets_for_agent and _register_extensions_for_agent are called when init --here --force is used on an existing project
• TestInitIntegrationFlag::test_init_here_without_force_does_not_reapply_presets — verifies the reapply block is not triggered on a fresh init without --force

Local Verification

• No project test command could be executed in this environment (no test runtime available). The fix was verified by code inspection against the analogous pattern in integration_upgrade() at _migrate_commands.py:889-900, which uses identical call signatures and has been working correctly since PR [bug-fix] Fix upgrade-overwrites-copilot-skills: pass force=True to extension skill re-registration after upgrade #3853.

Deviations from Assessment

None. The implementation exactly matches the preferred remediation described in the assessment, including the force=True guard, the call signatures (mirrored from integration_upgrade), and the import style (lazy inline import, consistent with init.py's existing patterns).

Risks & Review Notes

• Both _register_presets_for_agent and _register_extensions_for_agent are best-effort (they catch all exceptions internally) — a failure in preset/extension reapplication will emit a warning but will not abort the init operation.
• Calling these functions on a project with no presets/extensions installed is a no-op, so the force=True guard is defensive rather than strictly required, but it is cleaner and documents intent.
• The open question from the assessment (whether the same gap applies to specify integration install <key>) is out of scope for this fix; it would be a separate investigation.

Refs #3990 · cc @takaya0

• Fixes [Bug]: specify init --here --force does not reapply installed presets, leaving preset registry out of sync with disk #3990

Generated by 🛠️ Fix Bug from Labeled Issue for issue #3990 · 977.4 AIC · ⌖ 17 AIC · ⊞ 36.4K · ◷

[Copilot]

Pull request overview

Reapplies installed preset and extension artifacts after forced project reinitialization.

Changes:

• Adds forced artifact re-registration after integration setup.
• Adds CLI regression tests for forced and non-forced initialization.

Show a summary per file

File	Description
src/specify_cli/commands/init.py	Re-registers installed extensions and presets on forced initialization.
tests/integrations/test_cli.py	Tests re-registration guard behavior.

Review details

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• Files reviewed: 2/2 changed files
• Comments generated: 1
• Review effort level: Balanced

[mnriem]

Please address Copilot feedback

[Copilot]

Review details

Suppressed comments (2)

src/specify_cli/commands/init.py:642

• These re-registration helpers run before the new init-options.json is saved at line 754, although both resolve the active integration/mode from that file. On a forced re-init that changes integration or toggles command/skills mode, they therefore use stale state: extension skill registration explicitly skips when agent_name != active_agent, and preset rendering can target the previous agent. Move this block after save_init_options(...) so it composes artifacts for the integration and mode just initialized.

                if force:
                    from ..integrations._helpers import (
                        _register_extensions_for_agent,
                        _register_presets_for_agent,
                    )

tests/integrations/test_cli.py:1125

• These assertions only prove that mocked helpers were invoked, so the test passes even when registration is a no-op, targets stale init-options, or omits the extension force=True behavior. Add an end-to-end regression that installs a minimal preset/extension, force-reinitializes, and verifies the composed artifact remains on disk; include a changed integration or command/skills mode case to cover when the new init-options take effect.

        assert mock_presets.called, (
            "_register_presets_for_agent was not called during init --here --force"
        )
        assert mock_extensions.called, (
            "_register_extensions_for_agent was not called during init --here --force"
        )

• Files reviewed: 2/2 changed files
• Comments generated: 0 new
• Review effort level: Balanced