fix: address PR review — lazy init, assertions, deprecated flags

- _ensure_configs(): catch ImportError (not Exception), don't set
  _configs_loaded on failure so retries work
- Move _ensure_configs() before unregister loop (not inside it)
- Module-level try/except catches ImportError specifically
- Remove tautology assertion (or True) in test_extensions.py
- Strengthen preset provenance assertion to check source: field
- Mark --offline, --skip-tls, --debug, --github-token as hidden
  deprecated no-ops in init()

1086 tests pass.

Author: mnriem

src/specify_cli/__init__.py

@@ -851,11 +851,11 @@ def init(
     no_git: bool = typer.Option(False, "--no-git", help="Skip git repository initialization"),
     here: bool = typer.Option(False, "--here", help="Initialize project in the current directory instead of creating a new one"),
     force: bool = typer.Option(False, "--force", help="Force merge/overwrite when using --here (skip confirmation)"),
-    skip_tls: bool = typer.Option(False, "--skip-tls", help="Skip SSL/TLS verification (not recommended)"),
-    debug: bool = typer.Option(False, "--debug", help="Show verbose diagnostic output for network and extraction failures"),
-    github_token: str = typer.Option(None, "--github-token", help="GitHub token to use for API requests (or set GH_TOKEN or GITHUB_TOKEN environment variable)"),
+    skip_tls: bool = typer.Option(False, "--skip-tls", help="Deprecated (no-op). Previously: skip SSL/TLS verification.", hidden=True),
+    debug: bool = typer.Option(False, "--debug", help="Deprecated (no-op). Previously: show verbose diagnostic output.", hidden=True),
+    github_token: str = typer.Option(None, "--github-token", help="Deprecated (no-op). Previously: GitHub token for API requests.", hidden=True),
     ai_skills: bool = typer.Option(False, "--ai-skills", help="Install Prompt.MD templates as agent skills (requires --ai)"),
-    offline: bool = typer.Option(False, "--offline", help="Use assets bundled in the specify-cli package instead of downloading from GitHub (no network access required). Bundled assets will become the default in v0.6.0 and this flag will be removed."),
+    offline: bool = typer.Option(False, "--offline", help="Deprecated (no-op). All scaffolding now uses bundled assets.", hidden=True),
     preset: str = typer.Option(None, "--preset", help="Install a preset during initialization (by preset ID)"),
     branch_numbering: str = typer.Option(None, "--branch-numbering", help="Branch numbering strategy: 'sequential' (001, 002, ...) or 'timestamp' (YYYYMMDD-HHMMSS)"),
     integration: str = typer.Option(None, "--integration", help="Use the new integration system (e.g. --integration copilot). Mutually exclusive with --ai."),

src/specify_cli/agents.py

@@ -50,8 +50,11 @@ def __init_subclass__(cls, **kwargs: Any) -> None:
     @classmethod
     def _ensure_configs(cls) -> None:
         if not cls._configs_loaded:
-            cls._configs_loaded = True
-            cls.AGENT_CONFIGS = _build_agent_configs()
+            try:
+                cls.AGENT_CONFIGS = _build_agent_configs()
+                cls._configs_loaded = True
+            except ImportError:
+                pass  # Circular import during module init; retry on next access
 
     @staticmethod
     def parse_frontmatter(content: str) -> tuple[dict, str]:
@@ -510,8 +513,8 @@ def unregister_commands(
             registered_commands: Dict mapping agent names to command name lists
             project_root: Path to project root
         """
+        self._ensure_configs()
         for agent_name, cmd_names in registered_commands.items():
-            self._ensure_configs()
             if agent_name not in self.AGENT_CONFIGS:
                 continue
 
@@ -531,9 +534,10 @@ def unregister_commands(
 
 
 # Populate AGENT_CONFIGS after class definition.
-# The deferred import avoids circular import issues during module loading.
+# Catches ImportError from circular imports during module loading;
+# _configs_loaded stays False so the next explicit access retries.
 try:
     CommandRegistrar._ensure_configs()
-except Exception:
-    pass  # Silently defer to first explicit access
+except ImportError:
+    pass
 

tests/test_extensions.py

@@ -1040,7 +1040,6 @@ def test_register_commands_for_claude(self, extension_dir, project_dir):
         content = cmd_file.read_text()
         assert "description: Test hello command" in content
         assert "test-ext" in content
-        assert "test-ext" in content or True  # skill format uses metadata.source instead
 
     def test_command_with_aliases(self, project_dir, temp_dir):
         """Test registering a command with aliases."""

tests/test_presets.py

@@ -1785,6 +1785,7 @@ def test_self_test_registers_commands_for_claude(self, project_dir):
         assert cmd_file.exists(), "Skill not registered in .claude/skills/"
         content = cmd_file.read_text()
         assert "self-test" in content
+        assert "source:" in content  # skill frontmatter includes metadata.source
 
     def test_self_test_registers_commands_for_gemini(self, project_dir):
         """Test that installing self-test registers commands in .gemini/commands/ as TOML."""