feat(graph): Cypher-subset query engine -- query-graph command + MCP tool (closes #9)

README.md

@@ -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 (55 static + 13 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), 55 statically-defined tools + 13 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)
@@ -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

SKILL-QUICK.md

@@ -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)
@@ -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)
+- 13 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)
 

SKILL.md

@@ -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.
 ---

pyproject.toml

@@ -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"

scripts/commands/query_graph.py

@@ -0,0 +1,112 @@
+# @WHO:   scripts/commands/query_graph.py
+# @WHAT:  Cypher-subset graph query — MATCH/WHERE/RETURN/LIMIT over graph_nodes + graph_edges
+# @PART:  commands
+# @ENTRY: execute()
+
+"""
+Query-graph command — Cypher-subset structural queries over the code graph (issue #9).
+
+Agents can express structural questions in a single expressive query
+instead of chaining ``trace`` + ``impact`` + ``context`` tool calls.
+One query replaces 3-5 tool calls for typical structural questions
+("who calls handleRequest", "dead code with no callers", "classes
+inheriting from BaseModel").
+
+Supported Cypher subset (per issue #9 "minimal viable" scope):
+
+    MATCH (f:Function)-[:CALLS]->(g)
+    WHERE f.name = 'handleRequest'
+    RETURN g.name, g.file
+
+    MATCH (c:Class)-[:INHERITS]->(p)
+    WHERE p.name = 'BaseModel'
+    RETURN c.name
+
+    MATCH (f:Function)
+    WHERE NOT EXISTS { ()-[:CALLS]->(f) }
+    RETURN f.name                     -- dead code (no callers)
+
+Clauses: MATCH, WHERE, RETURN, LIMIT
+Predicates: =, !=, <, >, <=, >=, CONTAINS, IS NULL, IS NOT NULL,
+            EXISTS { pattern }, NOT EXISTS { pattern }, AND, OR, NOT
+Node labels: Function, Class, File, Module, Route, Type, Interface
+Edge types: CALLS, IMPORTS, DEFINES, INHERITS, IMPLEMENTS, USES_TYPE
+
+Read-only — no CREATE / SET / DELETE clauses. Default LIMIT 100, hard
+cap 1000 to prevent runaway queries.
+
+Example:
+    codelens query-graph \\
+        'MATCH (f:Function)-[:CALLS]->(g) WHERE f.name = \\'handleRequest\\' RETURN g.name, g.file' \\
+        /path/to/workspace
+
+    codelens query-graph --query 'MATCH (f:Function) WHERE NOT EXISTS { ()-[:CALLS]->(f) } RETURN f.name' /path/to/workspace
+"""
+
+from typing import Optional
+
+from commands import register_command
+from cypher_query_engine import query_graph, CypherParseError
+
+
+def add_args(parser):
+    """Add query-graph arguments to the parser."""
+    parser.add_argument(
+        "query",
+        help=(
+            "Cypher-subset query string. Must contain MATCH ... RETURN. "
+            "Example: \"MATCH (f:Function)-[:CALLS]->(g) WHERE f.name = 'handleRequest' RETURN g.name\""
+        ),
+    )
+    parser.add_argument(
+        "workspace", nargs="?", default=None,
+        help="Path to workspace root (auto-detected if omitted)",
+    )
+    parser.add_argument(
+        "--db-path", default=None,
+        help="Custom path for SQLite database file (default: <workspace>/.codelens/codelens.db)",
+    )
+    parser.add_argument(
+        "--explain", action="store_true",
+        help="Show the translated SQL and parameters without executing the query",
+    )
+
+
+def execute(args, workspace):
+    """Execute the query-graph command.
+
+    @FLOW: QUERY_GRAPH
+    @CALLS: cypher_query_engine.query_graph() -> result_dict
+    @MUTATES: none (read-only graph query)
+    """
+    db_path = getattr(args, "db_path", None)
+
+    if getattr(args, "explain", False):
+        # Parse + translate only, don't execute.
+        from cypher_query_engine import parse, translate
+        try:
+            ast = parse(args.query)
+            sql, params, ret = translate(ast)
+        except CypherParseError as e:
+            return {
+                "status": "error",
+                "error": f"Parse error: {e}",
+                "query": args.query,
+            }
+        return {
+            "status": "ok",
+            "query": args.query,
+            "sql": sql,
+            "params": params,
+            "return_items": [r.display_name() for r in ret],
+        }
+
+    return query_graph(args.query, workspace, db_path=db_path)
+
+
+register_command(
+    "query-graph",
+    "Cypher-subset structural query over graph_nodes + graph_edges (MATCH/WHERE/RETURN/LIMIT, read-only)",
+    add_args,
+    execute,
+)