feat(xrepo): cross-repo intelligence — multi-repo query via --additional-paths (closes #15)

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 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).
+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 72 CLI commands, an MCP server with 70 tools (54 static + 16 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
 
-- **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`)
+- **72 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 (70 Tools)** — Native AI agent integration via Model Context Protocol (JSON-RPC over stdio), 54 statically-defined tools + 16 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 (70 commands registered)
-│   ├── mcp_server.py              # MCP JSON-RPC server (68 tools)
+│   ├── codelens.py                # CLI entry point (72 commands registered)
+│   ├── mcp_server.py              # MCP JSON-RPC server (70 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

@@ -115,7 +115,7 @@ $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 70 Commands
+## All 72 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)
@@ -147,19 +147,19 @@ $CLI list --limit 5 --offset 10 --format compact            # → paginated + co
 ### Tooling (1)
 `plugin <install|list|search|update|info|validate>`
 
-**Total: 70 commands** (auto-registered via `commands/__init__.py`; rerun `python3 scripts/sync_command_count.py --apply` after adding/removing a command)
+**Total: 72 commands** (auto-registered via `commands/__init__.py`; rerun `python3 scripts/sync_command_count.py --apply` after adding/removing a command)
 
-## MCP Server (68 Tools)
+## MCP Server (70 Tools)
 
 Start the MCP server for AI agent integration:
 
 ```bash
 python3 scripts/codelens.py serve
 ```
 
-Exposes 68 tools as `codelens_<command>` (e.g., `codelens_query`, `codelens_taint`, `codelens_graph_schema`, `codelens_architecture`, `codelens_resolve_types`, `codelens_git_status`):
+Exposes 70 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`)
-- 13 dynamically-discovered tools (auto-discovered from `COMMAND_REGISTRY`; long-running `watch` and `serve` are excluded)
+- 16 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. 70 commands for AI-powered code analysis,
+  CodeLens — AI-Native Code Intelligence. 72 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 68 tools for AI agent integration.
+  fallback parsing. MCP server exposes 70 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 — 70 commands for AI-powered code analysis, security auditing, and quality scoring"
+description = "Live Codebase Reference Intelligence — 72 commands for AI-powered code analysis, security auditing, and quality scoring"
 readme = "README.md"
 license = {text = "MIT"}
 requires-python = ">=3.8"

scripts/commands/query.py

@@ -39,11 +39,42 @@ def add_args(parser):
                         help="Return all callers/callees (no limit)")
     parser.add_argument("--fuzzy", action="store_true",
                         help="Enable fuzzy/substring matching (case-insensitive)")
+    parser.add_argument(
+        "--additional-paths",
+        default=None,
+        metavar="PATHS",
+        help=(
+            "Comma-separated list of additional repo root paths to search "
+            "across (issue #15 cross-repo intelligence). When provided, the "
+            "query loads and merges registries from all repos and resolves "
+            "cross-repo call edges. Example: "
+            "'--additional-paths ../lib/shared,../services/worker'."
+        ),
+    )
 
 
 def execute(args, workspace):
     limit = None if getattr(args, 'all', False) else getattr(args, 'limit', 20)
     fuzzy = getattr(args, 'fuzzy', False)
+
+    # ── Cross-repo path (issue #15) ──
+    # When --additional-paths is provided, delegate to the cross-repo
+    # engine which merges registries from all repos and resolves
+    # cross-repo call edges. The result shape is compatible with the
+    # single-repo query result, so downstream formatting (compact, ai,
+    # etc.) works unchanged.
+    additional_paths_raw = getattr(args, 'additional_paths', None)
+    if additional_paths_raw:
+        from crossrepo_engine import query_cross_repo, _parse_additional_paths
+        additional_paths = _parse_additional_paths(additional_paths_raw)
+        result = query_cross_repo(
+            args.name, workspace, additional_paths,
+            fuzzy=fuzzy, limit=limit if limit else 20,
+        )
+        _attach_baseline_confidence(result, args.name, workspace)
+        return result
+
+    # ── Single-repo path (default, unchanged) ──
     result = cmd_query(args.name, workspace, args.domain, args.file, limit=limit, fuzzy=fuzzy)
     _attach_baseline_confidence(result, args.name, workspace)
     return result