Stage 6: Complete migration — remove legacy scaffold path (#1924) (#2063)

* Stage 6: Complete migration — remove legacy scaffold path (#1924)

Remove the legacy GitHub download and offline scaffold code paths.
All 26 agents now use the integration system exclusively.

Code removal (~1073 lines from __init__.py):
- download_template_from_github(), download_and_extract_template()
- scaffold_from_core_pack(), _locate_release_script()
- install_ai_skills(), _get_skills_dir (restored slim version for presets)
- _has_bundled_skills(), _migrate_legacy_kimi_dotted_skills()
- AGENT_SKILLS_MIGRATIONS, _handle_agent_skills_migration()
- _parse_rate_limit_headers(), _format_rate_limit_error()
- Three-way branch in init() collapsed to integration-only

Config derivation (single source of truth):
- AGENT_CONFIG derived from INTEGRATION_REGISTRY (replaced 180-line dict)
- CommandRegistrar.AGENT_CONFIGS derived from INTEGRATION_REGISTRY (replaced 160-line dict)
- Backward-compat constants kept for presets/extensions: SKILL_DESCRIPTIONS,
  NATIVE_SKILLS_AGENTS, DEFAULT_SKILLS_DIR

Release pipeline cleanup:
- Deleted create-release-packages.sh/.ps1 (948 lines of ZIP packaging)
- Deleted create-github-release.sh, generate-release-notes.sh
- Deleted simulate-release.sh, get-next-version.sh, update-version.sh
- Removed .github/workflows/scripts/ directory entirely
- release.yml is now self-contained: check, notes, release all inlined
- Install instructions use uv tool install with version tag

Test cleanup:
- Deleted test_ai_skills.py (tested removed functions)
- Deleted test_core_pack_scaffold.py (tested removed scaffold)
- Cleaned test_agent_config_consistency.py (removed 19 release-script tests)
- Fixed test_branch_numbering.py (removed dead monkeypatches)
- Updated auto-promote tests (verify files created, not tip messages)

1089 tests pass, 0 failures, ruff clean.

* fix: resolve merge conflicts with #2051 (claude as skills)

- Fix circular import: move CommandRegistrar import in claude
  integration to inside method bodies (was at module level)
- Lazy-populate AGENT_CONFIGS via _ensure_configs() to avoid
  circular import at class definition time
- Set claude registrar_config to .claude/commands (extension/preset
  target) since the integration handles .claude/skills in setup()
- Update tests from #2051 to match: registrar_config assertions,
  remove --integration tip assertions, remove install_ai_skills mocks

1086 tests pass.

* fix: properly preserve claude skills migration from #2051

Restore ClaudeIntegration.registrar_config to .claude/skills (not
.claude/commands) so extension/preset registrations write to the
correct skills directory.

Update tests that simulate claude setup to use .claude/skills and
check for SKILL.md layout. Some tests still need updating for the
full skills path — 10 remaining failures from the #2051 test
expectations around the extension/preset skill registration flow.

WIP: 1076/1086 pass.

* fix: properly handle SKILL.md paths in extension update rollback and tests

Fix extension update rollback using _compute_output_name() for SKILL.md
agents (converts dots to hyphens in skill directory names). Previously
the backup and cleanup code constructed paths with raw command names
(e.g. speckit.test-ext.hello/SKILL.md) instead of the correct computed
names (speckit-test-ext-hello/SKILL.md).

Test fixes for claude skills migration:
- Update claude tests to use .claude/skills paths and SKILL.md layout
- Use qwen (not claude) for skills-guard tests since claude's agent dir
  IS the skills dir — creating it triggers command registration
- Fix test_extension_command_registered_when_extension_present to check
  skills path format

1086 tests pass, 0 failures, ruff clean.

* 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.

* fix: remove deleted release scripts from pyproject.toml force-include

Removes force-include entries for create-release-packages.sh/.ps1
which were deleted but still referenced in [tool.hatch.build].

src/specify_cli/integrations/claude/__init__.py

@@ -7,7 +7,6 @@ from typing import Any
 
 import yaml
 
-from ...agents import CommandRegistrar
 from ..base import SkillsIntegration
 from ..manifest import IntegrationManifest
 
@@ -43,15 +42,18 @@ class ClaudeIntegration(SkillsIntegration):
             "description",
             f"Spec-kit workflow command: {template_name}",
         )
-        skill_frontmatter = CommandRegistrar.build_skill_frontmatter(
-            self.key,
-            skill_name,
-            description,
-            f"templates/commands/{template_name}.md",
+        skill_frontmatter = self._build_skill_fm(
+            skill_name, description, f"templates/commands/{template_name}.md"
         )
         frontmatter_text = yaml.safe_dump(skill_frontmatter, sort_keys=False).strip()
         return f"---\n{frontmatter_text}\n---\n\n{body.strip()}\n"
 
+    def _build_skill_fm(self, name: str, description: str, source: str) -> dict:
+        from specify_cli.agents import CommandRegistrar
+        return CommandRegistrar.build_skill_frontmatter(
+            self.key, name, description, source
+        )
+
     def setup(
         self,
         project_root: Path,
@@ -83,6 +85,7 @@ class ClaudeIntegration(SkillsIntegration):
 
         script_type = opts.get("script_type", "sh")
         arg_placeholder = self.registrar_config.get("args", "$ARGUMENTS")
+        from specify_cli.agents import CommandRegistrar
         registrar = CommandRegistrar()
         created: list[Path] = []