fix: isolate per-extension failures so one bad extension can't drop the rest

[PascalThuet]

What

ExtensionManager.register_enabled_extensions_for_agent iterates over enabled extensions with no per-extension error isolation. If registering one extension raised (e.g. an OSError writing a command file), the loop aborted and the exception propagated, so every subsequent enabled extension was silently skipped. The callers wrap the whole call in a single best-effort try/except, so the wholesale abort surfaced as one warning while the command still exited 0 — leaving the agent with only a prefix of its extensions registered.

This path is reached by integration switch and (since #2949 / #2886) integration install and integration upgrade.

Fix

Wrap the per-extension loop body in try/except: on failure, warn (naming the failing extension) and continue to the rest. The caller-level best-effort catch remains as a backstop.

Note the loop already guards the non-raising degraded cases — a manifest that fails to load is skipped (get_extension(...) is None → continue) and an empty registration result clears stale state — so this only adds isolation for genuine exceptions mid-loop.

Test

test_one_failing_extension_does_not_abort_the_rest installs two enabled extensions, forces the first-iterated one's registration to raise, and asserts the later extension still registers and the call does not propagate. Confirmed it fails without the fix.

Full suite: 3726 passed, 45 skipped locally.

Closes #2950

[Copilot]

Pull request overview

This PR improves robustness of extension command/skill registration by isolating failures per extension inside ExtensionManager.register_enabled_extensions_for_agent, ensuring one broken extension can’t prevent subsequent enabled extensions from registering.

Changes:

• Wrap per-extension registration work in try/except and emit a targeted warning on failure, then continue.
• Add a regression test proving that a failing extension does not abort registration of later extensions.

Show a summary per file

File	Description
src/specify_cli/extensions.py	Adds per-extension exception isolation during enabled-extension registration, warning and continuing on failures.
tests/test_extension_skills.py	Adds regression coverage ensuring one failing extension doesn’t prevent later extensions from registering.

Copilot's findings

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

[PascalThuet]

Updated on behalf of @PascalThuet by Codex (GPT-5).

Commit: 5cdbc5f

What changed:

• Addressed Copilot review 4506765356 by isolating _register_extension_skills() failures from successful command registration inside register_enabled_extensions_for_agent.
• Successful command registrations are now still persisted to registered_commands even when companion skill generation raises, preserving later cleanup/unregister behavior.
• Added regression coverage for the command-registration-succeeds / skill-registration-fails case.
• Merged current origin/main into the PR branch. The merge completed without manual conflicts.

Validation run locally:

• uv run pytest tests/test_extension_skills.py -q -> 53 passed
• uvx ruff check src/specify_cli/extensions.py tests/test_extension_skills.py -> passed
• git diff --check -> passed

GitHub now reports the PR as mergeable. gh pr checks currently reports no checks on the branch.

[Copilot]

Copilot's findings

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

[mnriem]

Please address Copilot feedback and rebase on upstream/main

[PascalThuet]

Updated on behalf of @PascalThuet by Codex (GPT-5).

Commit: c899cd3

What changed:

• Addressed the remaining Copilot feedback by replacing the skills-registration warning with wording that is accurate for both command-mode and skills-mode runs.
• Updated the regression assertion to use a stable substring from the new generic warning.
• Rebasing onto current origin/main resolved the merge conflict in src/specify_cli/extensions.py; GitHub now reports the PR as mergeable and behind_by: 0 against main.

Validation run locally:

• uv run pytest tests/test_extension_skills.py -q -> 54 passed
• uvx ruff check src/specify_cli/extensions.py tests/test_extension_skills.py -> passed
• git diff --check origin/main...HEAD -> passed

gh pr checks 2951 --repo github/spec-kit currently reports no checks on the branch.