[mnriem]

Description

Remove the duplicate process_registered_command() invocation in CommandRegistrar.register_commands(). Integration hooks now run once before argument and command-reference placeholder resolution, preventing repeated transformations of command frontmatter and bodies.

Testing

• Tested locally with uv run specify --help
• Ran existing tests with uv sync && uv run pytest
• Tested with a sample project (if applicable)

The existing-tests checkbox was validated using the documented worktree-local interpreter rather than bare uv run pytest:

• uv sync --extra test --quiet — passed.
• .venv/bin/python -m pytest tests/test_registered_command_hook.py -q before the fix — reproduced the three failures; four tests passed.
• .venv/bin/python -m pytest tests/test_registered_command_hook.py tests/integrations/test_integration_cline.py tests/integrations/test_integration_base_markdown.py tests/integrations/test_integration_base_toml.py tests/integrations/test_integration_base_skills.py -q after the fix — 59 passed.
• LC_ALL=en_US.UTF-8 .venv/bin/python -m pytest tests -n auto -q — 14,085 passed, 132 skipped, 63 warnings on macOS with Python 3.13.17.
• uv run specify --help — passed.
• git diff --check — passed.

Sample-project testing is not applicable to removing the duplicate hook invocation; existing registration tests exercise generated command output.

AI Disclosure

• I did not use AI assistance for this contribution
• I did use AI assistance (fill in the disclosure below)

AI disclosure: GitHub Copilot using GPT-6.1 Sol, in autonomous agent mode at the contributor's direction, investigated the failure, removed the duplicate call, ran automated checks, authored the commit, and drafted this PR. No human line-by-line review is claimed; the reasoning-effort setting was not exposed.

[Copilot]

🟢 Approval recommended

No active review issues remain for the change removing the duplicate integration-hook invocation.

No open issues 🎉

What changed in this PR

Fixes command registration so each integration hook runs once, preventing duplicate transformations of command frontmatter and bodies.

Changes:

• Removes the duplicate process_registered_command() invocation.
• Preserves hook execution before argument and command-reference placeholder resolution.

File	Description
src/​specify_cli/​agents.py	Removes the redundant integration hook call from CommandRegistrar.register_commands().

_{Review effort: Balanced (auto)}