CodeClone 2.1.0a1 — Structural Change Controller, Engineering Memory, and native agent integrations

.github/actions/codeclone/README.md

@@ -1,6 +1,7 @@
 # CodeClone GitHub Action
 
-Baseline-aware structural code quality analysis for Python with:
+**Structural Change Controller for AI-assisted Python development** — CI
+integration with:
 
 - configurable CI gating
 - SARIF upload for GitHub Code Scanning
@@ -82,9 +83,9 @@ jobs:
 | `python-version`        | `3.14`                          | Python version used to run the action                                                                             |
 | `package-version`       | `2.0.2`                         | CodeClone version from PyPI for remote installs; ignored when the action runs from the checked-out CodeClone repo |
 | `path`                  | `.`                             | Project root to analyze                                                                                           |
-| `json-path`             | `.cache/codeclone/report.json`  | JSON report output path                                                                                           |
+| `json-path`             | `.codeclone/report.json`  | JSON report output path                                                                                           |
 | `sarif`                 | `true`                          | Generate SARIF and try to upload it                                                                               |
-| `sarif-path`            | `.cache/codeclone/report.sarif` | SARIF output path                                                                                                 |
+| `sarif-path`            | `.codeclone/report.sarif` | SARIF output path                                                                                                 |
 | `pr-comment`            | `true`                          | Post or update a PR summary comment                                                                               |
 | `fail-on-new`           | `true`                          | Fail if new clone groups are detected                                                                             |
 | `fail-on-new-metrics`   | `false`                         | Fail if metrics regress vs baseline                                                                               |
@@ -182,4 +183,4 @@ Local/self-repo validation:
 
 - [CodeClone repository](https://github.com/orenlab/codeclone)
 - [Documentation](https://orenlab.github.io/codeclone/)
-- [SARIF integration](https://orenlab.github.io/codeclone/sarif/)
+- [SARIF integration](https://orenlab.github.io/codeclone/guide/integrations/sarif/export/)

.github/actions/codeclone/_action_impl.py

@@ -25,7 +25,7 @@
 from typing import Literal
 
 COMMENT_MARKER = "<!-- codeclone-report -->"
-DEFAULT_CODECLONE_PACKAGE_VERSION = "2.0.2"
+DEFAULT_CODECLONE_PACKAGE_VERSION = "2.1.0a1"
 
 
 @dataclass(frozen=True, slots=True)

.github/actions/codeclone/action.yml

@@ -18,7 +18,7 @@ inputs:
   package-version:
     description: "CodeClone version from PyPI for remote installs (ignored when the action runs from the checked-out CodeClone repo)"
     required: false
-    default: "2.0.2"
+    default: "2.1.0a1"
 
   path:
     description: "Project root"
@@ -28,7 +28,7 @@ inputs:
   json-path:
     description: "Canonical JSON report output path"
     required: false
-    default: ".cache/codeclone/report.json"
+    default: ".codeclone/report.json"
 
   sarif:
     description: "Generate SARIF and upload to Code Scanning"
@@ -38,7 +38,7 @@ inputs:
   sarif-path:
     description: "SARIF output path"
     required: false
-    default: ".cache/codeclone/report.sarif"
+    default: ".codeclone/report.sarif"
 
   pr-comment:
     description: "Post or update a PR summary comment"

.github/workflows/docs.yml

@@ -39,7 +39,7 @@ jobs:
         uses: actions/configure-pages@v5
 
       - name: Build docs site
-        run: uv run --with mkdocs --with mkdocs-material mkdocs build --strict
+        run: uv run --with zensical==0.0.43 zensical build --clean --strict
 
       - name: Generate sample report artifacts
         run: uv run python scripts/build_docs_example_report.py --output-dir site/examples/report/live

.github/workflows/integrations.yml

@@ -0,0 +1,126 @@
+name: integrations
+run-name: integrations • ${{ github.event_name }} • ${{ github.ref_name }}
+
+# Tests the IDE/agent integration surfaces that the main `tests` workflow does
+# not cover: the Node-based VS Code extension and Claude Desktop bundle, plus
+# the Codex and Cursor plugin contract tests. Runs only when an integration
+# surface (or the shared MCP tool snapshot the manifests are pinned to) changes.
+
+on:
+  push:
+    branches: [ "**" ]
+    paths:
+      - "extensions/**"
+      - "plugins/**"
+      - "tests/test_codex_plugin.py"
+      - "tests/test_cursor_plugin.py"
+      - "tests/test_cursor_plugin_hooks.py"
+      - "tests/fixtures/contract_snapshots/mcp_tool_schemas.json"
+      - ".github/workflows/integrations.yml"
+  pull_request:
+    paths:
+      - "extensions/**"
+      - "plugins/**"
+      - "tests/test_codex_plugin.py"
+      - "tests/test_cursor_plugin.py"
+      - "tests/test_cursor_plugin_hooks.py"
+      - "tests/fixtures/contract_snapshots/mcp_tool_schemas.json"
+      - ".github/workflows/integrations.yml"
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: integrations-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  vscode-extension:
+    name: VS Code extension
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: extensions/vscode-codeclone
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6.0.2
+
+      - name: Set up Node
+        uses: actions/setup-node@v4
+        with:
+          node-version: "20"
+          cache: npm
+          cache-dependency-path: extensions/vscode-codeclone/package-lock.json
+
+      - name: Install dependencies
+        run: npm ci
+
+      - name: Build, typecheck, and syntax-check
+        run: npm run check
+
+      - name: Unit tests
+        run: npm test
+
+  claude-desktop-bundle:
+    name: Claude Desktop bundle
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: extensions/claude-desktop-codeclone
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6.0.2
+
+      - name: Set up Node
+        uses: actions/setup-node@v4
+        with:
+          node-version: "20"
+          cache: npm
+          cache-dependency-path: extensions/claude-desktop-codeclone/package-lock.json
+
+      - name: Install dependencies
+        run: npm ci
+
+      - name: Syntax-check launcher and server
+        run: npm run check
+
+      - name: Unit tests
+        run: npm test
+
+      - name: Bundle build smoke
+        run: npm run pack
+
+  plugins:
+    name: Codex and Cursor plugins
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6.0.2
+
+      - name: Set up Python
+        uses: actions/setup-python@v6.2.0
+        with:
+          python-version: "3.14"
+          allow-prereleases: true
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: uv sync --extra dev --extra mcp
+
+      - name: Plugin contract tests
+        run: >-
+          uv run pytest -q
+          tests/test_codex_plugin.py
+          tests/test_cursor_plugin.py
+          tests/test_cursor_plugin_hooks.py
+
+      - name: Validate bundled plugin manifests
+        run: |
+          python3 -m json.tool plugins/codeclone/.codex-plugin/plugin.json > /dev/null
+          python3 -m json.tool plugins/codeclone/.mcp.json > /dev/null
+          python3 -m json.tool .agents/plugins/marketplace.json > /dev/null

.github/workflows/tests.yml

@@ -35,7 +35,7 @@ jobs:
           enable-cache: true
 
       - name: Install dependencies
-        run: uv sync --extra dev --extra mcp
+        run: uv sync --all-extras
 
       - name: Run tests
         # Smoke CLI tests intentionally disable subprocess coverage collection
@@ -67,10 +67,10 @@ jobs:
           enable-cache: true
 
       - name: Install dependencies
-        run: uv sync --extra dev --extra mcp
+        run: uv sync --all-extras
 
       - name: Ruff
         run: uv run ruff check .
 
       - name: Mypy
-        run: uv run mypy .
+        run: uv run mypy

.gitignore

@@ -22,12 +22,14 @@ site/
 
 # Tool caches
 .cache/
+.codeclone/
 .codeclone-cache/
 .codeclone-baseline.json.bak
 
 # IDE
 .idea/
 .vscode/
+/.cursor/
 
 # OS
 .DS_Store
@@ -45,3 +47,8 @@ extensions/vscode-codeclone/node_modules
 /scripts/refactor_guard.sh
 /docs/refactoring-spec.md
 /smoke_cli.sh
+/codeclone-v2.1-roadmap.md
+/specs/
+/coverage.json
+/benchmarks/memory_semantic_eval.md
+/scripts/commit_memory_phases.sh

.pre-commit-config.yaml

@@ -1,4 +1,4 @@
-default_install_hook_types: [ pre-commit, pre-push ]
+default_install_hook_types: [pre-commit, pre-push]
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -10,46 +10,62 @@ repos:
       - id: check-added-large-files
       - id: check-toml
       - id: check-yaml
+      - id: check-json
+      - id: check-ast
+      - id: debug-statements
+      - id: check-case-conflict
+      - id: check-symlinks
+      - id: destroyed-symlinks
+      - id: detect-private-key
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: forbid-submodules
 
   - repo: local
     hooks:
       - id: ruff-format
         name: Ruff (format)
-        entry: ruff format .
+        entry: uv run ruff format .
         language: system
         pass_filenames: false
-        types: [ python ]
-        stages: [ pre-commit ]
+        stages: [pre-commit]
 
       - id: ruff-check
         name: Ruff (lint)
-        entry: ruff check .
+        entry: uv run ruff check .
         language: system
         pass_filenames: false
-        types: [ python ]
-        stages: [ pre-commit ]
+        stages: [pre-commit]
 
       - id: mypy
         name: Mypy
-        entry: mypy
+        entry: uv run mypy
         language: system
         pass_filenames: false
-        types: [ python ]
-        stages: [ pre-commit ]
+        always_run: true
+        stages: [pre-commit]
 
       - id: codeclone
         name: CodeClone
-        entry: codeclone
+        entry: uv run codeclone
         language: system
         pass_filenames: false
-        args: [ ".", "--ci" ]
-        types: [ python ]
-        stages: [ pre-commit ]
+        args: [".", "--ci"]
+        always_run: true
+        stages: [pre-commit]
 
       - id: pytest
         name: Pytest
-        entry: pytest -q
+        entry: uv run pytest -q --cov=codeclone --cov-report=term-missing --cov-fail-under=99
         language: system
         pass_filenames: false
-        types: [ python ]
-        stages: [ pre-push ]
+        always_run: true
+        stages: [pre-push]
+
+      - id: lint-admonitions
+        name: Lint admonitions
+        entry: uv run scripts/lint_admonitions.py docs/ --fix
+        language: system
+        pass_filenames: false
+        files: ^docs/.*\.md$
+        stages: [ pre-commit ]