fix(sync): sync command count to 77 after rebase on main (closes #173)

Issue #173: PR #166 was written when main had 70 commands. After rebasing
on latest main (which merged orient #165, affected #142, and others),
the runtime COMMAND_REGISTRY now reports 77 commands.

Ran sync_command_count.py --apply to regenerate all count references:
- README.md: 5 substitutions
- SKILL-QUICK.md: 5 substitutions
- SKILL.md: 2 substitutions
- pyproject.toml: 1 substitution
- scripts/graph_model.py: 1 substitution
- skill.json: 1 substitution

Also resolved rebase conflicts in:
- scripts/mcp_server.py: merged Phase 1 (staleness) + Phase 4 (worktree)
  banner methods — both coexist on the MCP server
- scripts/sync/__init__.py: merged worktree (Phase 4) + pending (Phase 1)
  exports into unified __all__

Pre-existing finding (NOT caused by this PR): the 'affected' command
(PR #142, already on main) uses -f for --filter, which conflicts with
the global --format/-f flag added by codelens.py. This breaks ALL CLI
invocations that trigger argparse registration (e.g. 'codelens affected
--help'). Flagged for BOS — separate issue needed.

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 71 CLI commands, an MCP server with 69 tools (54 static + 15 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 77 CLI commands, an MCP server with 75 tools (56 static + 19 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
 
-- **71 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 (69 Tools)** — Native AI agent integration via Model Context Protocol (JSON-RPC over stdio), 54 statically-defined tools + 15 dynamically discovered, every tool accepts a `format` parameter (`json`/`markdown`/`ai`/`sarif`/`compact`)
+- **77 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 (75 Tools)** — Native AI agent integration via Model Context Protocol (JSON-RPC over stdio), 56 statically-defined tools + 19 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 (71 commands registered)
-│   ├── mcp_server.py              # MCP JSON-RPC server (69 tools)
+│   ├── codelens.py                # CLI entry point (77 commands registered)
+│   ├── mcp_server.py              # MCP JSON-RPC server (75 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

@@ -116,7 +116,7 @@ $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 71 Commands
+## All 77 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)
@@ -148,19 +148,19 @@ $CLI list --limit 5 --offset 10 --format compact            # → paginated + co
 ### Tooling (1)
 `plugin <install|list|search|update|info|validate>`
 
-**Total: 71 commands** (auto-registered via `commands/__init__.py`; rerun `python3 scripts/sync_command_count.py --apply` after adding/removing a command)
+**Total: 77 commands** (auto-registered via `commands/__init__.py`; rerun `python3 scripts/sync_command_count.py --apply` after adding/removing a command)
 
-## MCP Server (69 Tools)
+## MCP Server (75 Tools)
 
 Start the MCP server for AI agent integration:
 
 ```bash
 python3 scripts/codelens.py serve
 ```
 
-Exposes 69 tools as `codelens_<command>` (e.g., `codelens_query`, `codelens_taint`, `codelens_graph_schema`, `codelens_architecture`, `codelens_resolve_types`, `codelens_git_status`):
+Exposes 75 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`)
-- 15 dynamically-discovered tools (auto-discovered from `COMMAND_REGISTRY`; long-running `watch` and `serve` are excluded)
+- 19 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. 71 commands for AI-powered code analysis,
+  CodeLens — AI-Native Code Intelligence. 77 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 69 tools for AI agent integration.
+  fallback parsing. MCP server exposes 75 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 — 71 commands for AI-powered code analysis, security auditing, and quality scoring"
+description = "Live Codebase Reference Intelligence — 77 commands for AI-powered code analysis, security auditing, and quality scoring"
 readme = "README.md"
 license = {text = "MIT"}
 requires-python = ">=3.8"

scripts/graph_model.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 71 existing CLI commands continue to work unchanged.
+- All 77 existing CLI commands continue to work unchanged.
 
 Schema:
     graph_nodes(

skill.json

@@ -1,7 +1,7 @@
 {
   "name": "codelens",
   "version": "8.2.0",
-  "description": "Live Codebase Reference Intelligence. 71 commands for AI-powered code analysis, security auditing, quality scoring, and pre-write safety checks. Supports 28+ languages with regex+AST hybrid parsing. Must activate before writing/editing/deleting any class, id, or function.",
+  "description": "Live Codebase Reference Intelligence. 77 commands for AI-powered code analysis, security auditing, quality scoring, and pre-write safety checks. Supports 28+ languages with regex+AST hybrid parsing. Must activate before writing/editing/deleting any class, id, or function.",
   "author": "codelens",
   "command_categories": {
     "setup": [