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2 changes: 1 addition & 1 deletion .github/workflows/codelens-ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ jobs:
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install tree-sitter pyyaml pytest pytest-cov
pip install tree-sitter pyyaml pytest pytest-cov pygls lsprotocol
# Install optional grammar packages for full parser coverage
pip install tree-sitter-python tree-sitter-javascript tree-sitter-html tree-sitter-css || true
pip install tree-sitter-typescript tree-sitter-rust || true
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10 changes: 5 additions & 5 deletions README.md
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Expand Up @@ -2,12 +2,12 @@

> **Before an AI writes a new class/id/function, CodeLens must be checked. This is not optional.**

CodeLens is an AI-native code intelligence platform that gives AI agents **full visibility** into a codebase before they write any code. It prevents collision, overwrite of existing logic, security vulnerabilities, and dead code through 68 CLI commands, an MCP server with 66 tools (54 static + 12 dynamic), AST-based taint analysis, live CVE/OSV scanning, a plugin system with OWASP Top 10 + Compliance rule packs, a true graph data model (nodes + edges) for structural code queries, and token-efficient `--format compact` output for high-volume agent workflows (issue #17).
CodeLens is an AI-native code intelligence platform that gives AI agents **full visibility** into a codebase before they write any code. It prevents collision, overwrite of existing logic, security vulnerabilities, and dead code through 70 CLI commands, an MCP server with 68 tools (54 static + 14 dynamic), AST-based taint analysis, live CVE/OSV scanning, a plugin system with OWASP Top 10 + Compliance rule packs, a true graph data model (nodes + edges) for structural code queries, and token-efficient `--format compact` output for high-volume agent workflows (issue #17).

## Features

- **68 CLI Commands** — From basic scan/query to AST taint analysis, CVE scanning, plugin management, auto-fix, dashboards, CI/CD quality gates, and `graph-schema` for cheap graph-shape introspection
- **MCP Server (66 Tools)** — Native AI agent integration via Model Context Protocol (JSON-RPC over stdio), 54 statically-defined tools + 12 dynamically discovered, every tool accepts a `format` parameter (`json`/`markdown`/`ai`/`sarif`/`compact`)
- **70 CLI Commands** — From basic scan/query to AST taint analysis, CVE scanning, plugin management, auto-fix, dashboards, CI/CD quality gates, and `graph-schema` for cheap graph-shape introspection
- **MCP Server (68 Tools)** — Native AI agent integration via Model Context Protocol (JSON-RPC over stdio), 54 statically-defined tools + 14 dynamically discovered, every tool accepts a `format` parameter (`json`/`markdown`/`ai`/`sarif`/`compact`)
- **Token-Efficient Compact Output (v8.2, issue #17)** — `--format compact` produces single-char-key JSON with abbreviated types, omitted null fields, and relative paths — ~50% smaller than `json` on real trace output. Combined with `--limit`/`--offset` pagination, 5 structural queries now cost <5k tokens (down from 30-80k)
- **AST Taint Engine** — Tree-sitter based taint analysis with return-value propagation, scope hierarchy, and branch condition refinement
- **Live CVE/OSV Scanning** — Real-time vulnerability data from OSV.dev API with SQLite cache, 9 ecosystems (PyPI, npm, crates.io, Go, Maven, NuGet, RubyGems, Pub, Hex)
Expand Down Expand Up @@ -225,8 +225,8 @@ codelens/
│ ├── changelog.md # Older changelog (per-version highlights)
│ └── agent-integration.md # AI agent integration guide
├── scripts/
│ ├── codelens.py # CLI entry point (68 commands registered)
│ ├── mcp_server.py # MCP JSON-RPC server (66 tools)
│ ├── codelens.py # CLI entry point (70 commands registered)
│ ├── mcp_server.py # MCP JSON-RPC server (68 tools)
│ ├── registry.py # Registry read/write/build
│ ├── persistent_registry.py # SQLite persistent storage (WAL mode)
│ ├── base_parser.py # Base tree-sitter parser
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10 changes: 5 additions & 5 deletions SKILL-QUICK.md
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Expand Up @@ -114,7 +114,7 @@ $CLI list --limit 5 --offset 10 --format compact # → paginated + co
| "Cross-file taint" | `dataflow` | `taint` (taint is single-file, AST-deep) |
| "Auto-fix issues" | `fix` | `check` (check just gates, doesn't fix) |

## All 68 Commands
## All 70 Commands

### Setup & Lifecycle (8+)
`init` · `scan [--incremental] [--max-files N] [--full]` · `registry-validate` · `detect` · `watch [--debounce SECS] [--git-mode] [--interval SECS]` · `git-status` · `migrate` · `serve` · `lsp-status` (issue #33: `codelens --lsp-status` top-level flag is an alias of `codelens lsp-status` — both delegate to `hybrid_engine.get_lsp_status()` and return the identical payload)
Expand Down Expand Up @@ -146,19 +146,19 @@ $CLI list --limit 5 --offset 10 --format compact # → paginated + co
### Tooling (1)
`plugin <install|list|search|update|info|validate>`

**Total: 68 commands** (auto-registered via `commands/__init__.py`; rerun `python3 scripts/sync_command_count.py --apply` after adding/removing a command)
**Total: 70 commands** (auto-registered via `commands/__init__.py`; rerun `python3 scripts/sync_command_count.py --apply` after adding/removing a command)

## MCP Server (66 Tools)
## MCP Server (68 Tools)

Start the MCP server for AI agent integration:

```bash
python3 scripts/codelens.py serve
```

Exposes 66 tools as `codelens_<command>` (e.g., `codelens_query`, `codelens_taint`, `codelens_graph_schema`, `codelens_architecture`, `codelens_resolve_types`, `codelens_git_status`):
Exposes 68 tools as `codelens_<command>` (e.g., `codelens_query`, `codelens_taint`, `codelens_graph_schema`, `codelens_architecture`, `codelens_resolve_types`, `codelens_git_status`):
- 50 statically-defined tools (full JSON schemas in `mcp_server.py`)
- 12 dynamically-discovered tools (auto-discovered from `COMMAND_REGISTRY`; long-running `watch` and `serve` are excluded)
- 14 dynamically-discovered tools (auto-discovered from `COMMAND_REGISTRY`; long-running `watch` and `serve` are excluded)
- Every tool accepts a `format` parameter (`json`/`markdown`/`ai`/`sarif`/`compact`). Use `format: "compact"` for token-efficient responses (~50% smaller than `json`).
- `watch` and `serve` itself are excluded (long-running)

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4 changes: 2 additions & 2 deletions SKILL.md
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@@ -1,10 +1,10 @@
---
name: codelens
description: >
CodeLens — AI-Native Code Intelligence. 68 commands for AI-powered code analysis,
CodeLens — AI-Native Code Intelligence. 70 commands for AI-powered code analysis,
security auditing, quality scoring, AST-based taint analysis, live CVE scanning,
and pre-write safety checks. Supports 28+ languages with tree-sitter + regex
fallback parsing. MCP server exposes 66 tools for AI agent integration.
fallback parsing. MCP server exposes 68 tools for AI agent integration.
For quick command reference with validated output schemas, see SKILL-QUICK.md.
For version history, see CHANGELOG.md.
---
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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
[project]
name = "codelens"
version = "8.2.0"
description = "Live Codebase Reference Intelligence — 68 commands for AI-powered code analysis, security auditing, and quality scoring"
description = "Live Codebase Reference Intelligence — 70 commands for AI-powered code analysis, security auditing, and quality scoring"
readme = "README.md"
license = {text = "MIT"}
requires-python = ">=3.8"
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21 changes: 12 additions & 9 deletions scripts/codelens.py
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Expand Up @@ -46,7 +46,6 @@
python3 codelens.py ask <question> [workspace] # Ask a natural language question about the codebase
python3 codelens.py migrate <workspace> # Migrate JSON registry to SQLite
python3 codelens.py lsp-status # Check LSP server availability
python3 codelens.py lsp [--rule-file x.yaml] [--tcp --port 2087] # Run as native LSP 3.17 server (issue #48)
python3 codelens.py taint <workspace> # Semantic taint analysis for vulnerability detection
python3 codelens.py dashboard <workspace> # Generate HTML visualization dashboard
python3 codelens.py history <workspace> # Show historical trend data
Expand Down Expand Up @@ -1278,14 +1277,18 @@ def main():
logger.warning(f"Suppression processing failed: {e}", exc_info=True)

# ─── Format and print output ──
# doctor (issue #64) prints its own human-readable text table when
# ``--format text`` is used, and signals via ``_doctor_printed_text``
# so the dispatcher skips the generic JSON formatter (which would
# otherwise dump the result dict a second time). In ``--format json``
# mode doctor does NOT print itself, and the normal formatter handles
# the JSON serialization.
if not (args.command == "doctor" and isinstance(result, dict)
and result.get("_doctor_printed_text")):
# Some commands (doctor issue #64 Phase 1, sessions issue #64
# Phase 2) print their own human-readable output directly and
# signal via ``_doctor_printed_text`` / ``_sessions_printed_text``
# so the dispatcher skips the generic JSON formatter (which
# would otherwise dump the result dict a second time). In
# ``--format json`` mode these commands do NOT print themselves,
# and the normal formatter handles the JSON serialization.
_already_printed = (
isinstance(result, dict)
and (result.get("_doctor_printed_text") or result.get("_sessions_printed_text"))
)
if not (args.command in ("doctor", "sessions") and _already_printed):
print(format_output(result, args.format, format_command, workspace))

# ─── Exit codes for CI-quality-gate commands ──
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