chore(commands): remove deprecated validate command, update count to 63 (closes #100)

Author: Wolfvin

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 64 CLI commands, an MCP server with 62 tools (51 static + 11 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 63 CLI commands, an MCP server with 61 tools (50 static + 11 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
 
-- **64 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 (62 Tools)** — Native AI agent integration via Model Context Protocol (JSON-RPC over stdio), 51 statically-defined tools + 11 dynamically discovered, every tool accepts a `format` parameter (`json`/`markdown`/`ai`/`sarif`/`compact`)
+- **63 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 (61 Tools)** — Native AI agent integration via Model Context Protocol (JSON-RPC over stdio), 50 statically-defined tools + 11 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)
@@ -82,7 +82,7 @@ python3 scripts/codelens.py query "myFunction" --lite
 |---------|-------------|
 | `init [workspace]` | Initialize `.codelens` config with auto-detected frameworks |
 | `scan [workspace] [--incremental] [--full] [--max-files N]` | Scan workspace and build registry |
-| `validate [workspace]` | Validate registry vs file system |
+| `registry-validate [workspace]` | Validate registry vs file system |
 | `detect [workspace]` | Detect frameworks and show recommended config |
 | `watch [workspace] [--git-mode] [--interval SECS]` | Start file watcher (default: watchdog; `--git-mode` polls `git diff --name-only`) |
 | `git-status [workspace]` | Show git-aware scan state: HEAD SHA, last-indexed SHA, changed files, re-scan recommendation |
@@ -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 (64 commands registered)
-│   ├── mcp_server.py              # MCP JSON-RPC server (62 tools)
+│   ├── codelens.py                # CLI entry point (63 commands registered)
+│   ├── mcp_server.py              # MCP JSON-RPC server (61 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

@@ -114,10 +114,10 @@ $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 64 Commands
+## All 63 Commands
 
 ### Setup & Lifecycle (8+)
-`init` · `scan [--incremental] [--max-files N] [--full]` · `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)
+`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)
 
 ### Pre-Write Safety (5)
 `query "name" [--domain ...] [--fuzzy]` · `impact "name" [--action modify|delete]` · `refactor-safe "name" [--action rename|move]` · `guard (--pre|--post) --file PATH` · `check [--severity ...] [--max-findings N]`
@@ -146,18 +146,18 @@ $CLI list --limit 5 --offset 10 --format compact            # → paginated + co
 ### Tooling (1)
 `plugin <install|list|search|update|info|validate>`
 
-**Total: 64 commands** (auto-registered via `commands/__init__.py`; rerun `python3 scripts/sync_command_count.py --apply` after adding/removing a command)
+**Total: 63 commands** (auto-registered via `commands/__init__.py`; rerun `python3 scripts/sync_command_count.py --apply` after adding/removing a command)
 
-## MCP Server (62 Tools)
+## MCP Server (61 Tools)
 
 Start the MCP server for AI agent integration:
 
 ```bash
 python3 scripts/codelens.py serve
 ```
 
-Exposes 62 tools as `codelens_<command>` (e.g., `codelens_query`, `codelens_taint`, `codelens_graph_schema`, `codelens_architecture`, `codelens_resolve_types`, `codelens_git_status`):
-- 51 statically-defined tools (full JSON schemas in `mcp_server.py`)
+Exposes 61 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`)
 - 11 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. 64 commands for AI-powered code analysis,
+  CodeLens — AI-Native Code Intelligence. 63 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 62 tools for AI agent integration.
+  fallback parsing. MCP server exposes 61 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 — 64 commands for AI-powered code analysis, security auditing, and quality scoring"
+description = "Live Codebase Reference Intelligence — 63 commands for AI-powered code analysis, security auditing, and quality scoring"
 readme = "README.md"
 license = {text = "MIT"}
 requires-python = ">=3.8"

scripts/codelens.py

@@ -18,7 +18,7 @@
     python3 codelens.py circular <workspace>           # Detect circular dependencies
     python3 codelens.py context <name> <workspace>     # Get rich symbol context
     python3 codelens.py dependents <file> <workspace>  # Module-level import tracking
-    python3 codelens.py validate <workspace>           # Validate registry vs file system
+    python3 codelens.py registry-validate <workspace>  # Validate registry vs file system
     python3 codelens.py dataflow <workspace>           # Trace data flow source→sink
     python3 codelens.py smell <workspace>              # Detect code smells
     python3 codelens.py side-effect <workspace> [--name func]  # Analyze function side effects
@@ -1038,7 +1038,7 @@ def main():
         "secrets", "dataflow", "vuln-scan", "env-check", "entrypoints",
         "api-map", "state-map", "handbook", "analyze", "test-map",
         "stack-trace", "config-drift", "type-infer", "ownership",
-        "regex-audit", "a11y", "css-deep", "diff", "ask", "validate",
+        "regex-audit", "a11y", "css-deep", "diff", "ask",
         "taint", "dashboard", "history",
     }
 

scripts/commands/registry_validate.py

@@ -1,9 +1,9 @@
 """registry-validate command — Validate registry against file system.
 
 Renamed from `validate` in v8.x to make room for `rule-validate` (rule YAML
-validation). The old `validate` command name still works as a deprecated alias
-(see ``scripts/commands/validate.py``) but prints a one-line stderr warning
-and will be removed in a future release.
+validation). The deprecated `validate` alias was removed in issue #100 —
+use `registry-validate` for registry checks, or `rule-validate` for rule
+YAML validation.
 """
 
 import sys
@@ -38,7 +38,7 @@ def execute(args, workspace):
 
 register_command(
     "registry-validate",
-    "Validate registry against file system (renamed from `validate`)",
+    "Validate registry against file system",
     add_args,
     execute,
 )

scripts/commands/validate.py

@@ -88,8 +88,6 @@ def to_markdown(data: Any, command: str = "") -> str:
         _md_diff(data, lines)
     elif command == "dependents":
         _md_dependents(data, lines)
-    elif command == "validate":
-        _md_validate(data, lines)
     elif command == "dataflow":
         _md_dataflow(data, lines)
     elif command == "test-map":
@@ -1217,40 +1215,6 @@ def _md_dependents(data: Dict, lines: list) -> None:
         lines.append("")
 
 
-def _md_validate(data: Dict, lines: list) -> None:
-    """Markdown for validate command."""
-    total = data.get("total_issues", 0)
-    summary = data.get("summary", {})
-    rec = data.get("recommendation", "")
-    lines.append("## Registry Validation")
-    lines.append("")
-    icon = "PASS" if total == 0 else "FAIL"
-    lines.append(f"**Status:** {icon} ({total} issues)")
-    lines.append("")
-    lines.append(f"- Missing files: {summary.get('missing_files', 0)}")
-    lines.append(f"- Unregistered files: {summary.get('unregistered_files', 0)}")
-    lines.append(f"- Stale references: {summary.get('stale_references', 0)}")
-    lines.append(f"- Orphan entries: {summary.get('orphan_entries', 0)}")
-    lines.append("")
-    issues = data.get("issues", {})
-    if issues:
-        for cat in ["missing_files", "unregistered_files", "stale_references", "orphan_entries"]:
-            items = issues.get(cat, [])
-            if items:
-                lines.append(f"### {cat.replace('_', ' ').title()}")
-                for item in items[:10]:
-                    if isinstance(item, dict):
-                        lines.append(f"- `{item.get('file', item.get('path', ''))}` — {item.get('reason', '')}")
-                    else:
-                        lines.append(f"- `{item}`")
-                if len(items) > 10:
-                    lines.append(f"- ... and {len(items) - 10} more")
-                lines.append("")
-    if rec:
-        lines.append(f"**Recommendation:** {rec}")
-        lines.append("")
-
-
 def _md_dataflow(data: Dict, lines: list) -> None:
     """Markdown for dataflow command."""
     stats = data.get("stats", {})

scripts/formatters/markdown.py

@@ -13,7 +13,7 @@
 - New tables `graph_nodes` and `graph_edges` are additive (prefixed `graph_`
   to avoid colliding with any existing table name).
 - The flat registry tables and JSON files are untouched.
-- All 64 existing CLI commands continue to work unchanged.
+- All 63 existing CLI commands continue to work unchanged.
 
 Schema:
     graph_nodes(

scripts/graph_model.py

@@ -4,7 +4,7 @@
 
 Implements the MCP specification (2025-03-26) over stdio (JSON-RPC 2.0).
 Provides persistent server mode with in-memory registry caching, sub-millisecond
-query latency after initial scan, and automatic tool discovery for all 64 CodeLens commands.
+query latency after initial scan, and automatic tool discovery for all 63 CodeLens commands.
 
 Usage:
     python3 codelens.py serve                        # Start MCP server (stdio transport)
@@ -664,19 +664,6 @@
             "required": ["workspace"]
         }
     },
-    "validate": {
-        "description": "Validate registry against file system. Detect stale registry entries.",
-        "parameters": {
-            "type": "object",
-            "properties": {
-                "workspace": {
-                    "type": "string",
-                    "description": "Path to workspace root directory"
-                }
-            },
-            "required": ["workspace"]
-        }
-    },
     "detect": {
         "description": "Detect frameworks and technologies used in the project.",
         "parameters": {