docs: fix stale codegraph check flag names across README and guides (#1984)

README.md

@@ -350,10 +350,10 @@ codegraph batch --json targets.json   # Batch from a JSON file
 codegraph check                             # Run manifesto rules on whole codebase
 codegraph check --staged                    # Check staged changes (diff predicates)
 codegraph check --staged --rules            # Run both diff predicates AND manifesto rules
-codegraph check --no-new-cycles             # Fail if staged changes introduce cycles
-codegraph check --max-complexity 30         # Fail if any function exceeds complexity threshold
-codegraph check --max-blast-radius 50       # Fail if blast radius exceeds limit
-codegraph check --no-boundary-violations    # Fail on architecture boundary violations
+codegraph check --staged --cycles           # Fail if staged changes introduce cycles
+codegraph check --staged --blast-radius 50  # Fail if blast radius exceeds limit
+codegraph check --staged --boundaries       # Fail on architecture boundary violations
+codegraph check --staged --signatures       # Fail if an exported declaration's line was modified
 codegraph check main                        # Check current branch vs main
 ```
 

docs/contributing/harness-engineering.md

@@ -41,7 +41,7 @@ Zero-tolerance enforcement: the agent cannot proceed until all checks pass. No w
 ```bash
 # Example: codegraph pre-commit gate
 codegraph build
-codegraph check --staged --no-new-cycles --max-blast-radius 50 -T
+codegraph check --staged --cycles --blast-radius 50 -T
 ```
 
 ### Layer 2: AI Review
@@ -119,7 +119,7 @@ With codegraph, this is built-in:
 
 ```bash
 # codegraph check provides actionable output
-codegraph check --staged --no-new-cycles --max-blast-radius 50 -T
+codegraph check --staged --cycles --blast-radius 50 -T
 # Output: "Cycle detected: A -> B -> C -> A. Break the cycle by..."
 # Output: "Blast radius 67 exceeds threshold 50. Function X affects..."
 ```
@@ -154,7 +154,7 @@ Types -> Config -> Repo -> Service -> Runtime -> UI
 ```
 
 **Enforcement tools:**
-- `codegraph check --no-boundary-violations` — blocks imports that violate layer direction
+- `codegraph check --staged --boundaries` — blocks imports that violate layer direction
 - `codegraph cycles` — detects circular dependencies
 - Custom ESLint rules or `dependency-cruiser` for additional constraints
 - CI gates that fail the build on violations
@@ -259,7 +259,7 @@ Codegraph already implements most of these practices. Here's how they map:
 |---|---|
 | Deterministic guardrails | `codegraph check` pre-commit gates, cycle detection, blast radius thresholds |
 | Remediation-focused errors | `codegraph check` output includes what violated and where |
-| Mechanical architecture | `codegraph check --no-boundary-violations`, `codegraph cycles` |
+| Mechanical architecture | `codegraph check --staged --boundaries`, `codegraph cycles` |
 | Silent success / loud failure | Claude Code hooks exit silently on success |
 | AGENTS.md | `CLAUDE.md` with codegraph workflow commands |
 | Progress tracking | Titan Paradigm skills with state files |
@@ -274,7 +274,7 @@ To add harness engineering to an existing codegraph project:
 1. **Create `CLAUDE.md`** with build commands and your top 5 failure-driven rules
 2. **Add pre-commit hooks** using codegraph check:
    ```bash
-   codegraph check --staged --no-new-cycles --max-blast-radius 50 -T
+   codegraph check --staged --cycles --blast-radius 50 -T
    ```
 3. **Configure CI gates** with `codegraph check -T` in your pipeline
 4. **Set up Claude Code hooks** — see [Claude Code Hooks Guide](../examples/claude-code-hooks/README.md) for ready-to-use scripts

docs/examples/CLI.md

@@ -498,7 +498,7 @@ Cycles whose only closing edge is a low-confidence dynamic call (resolved via
 a resolver heuristic rather than confirmed statically) are marked
 `[speculative]` rather than reported as confirmed structural cycles. Pass
 `--exclude-speculative` to drop them from the output entirely, or `--json` to
-get a `speculative: boolean` field per cycle. `codegraph check --cycles` and
+get a `speculative: boolean` field per cycle. `codegraph check --staged --cycles` and
 the manifesto `noCycles` rule ignore speculative-only cycles by default (see
 `check.excludeSpeculativeCycles` in [configuration](../guides/configuration.md)).
 
@@ -1172,43 +1172,46 @@ Configurable pass/fail gates. Exit code 0 = pass, 1 = fail.
 - `check --staged --rules` — runs both diff predicates AND manifesto rules
 
 ```bash
-codegraph check --staged --no-new-cycles --max-complexity 30
+codegraph check --staged --cycles
 ```
 
 ```
 # Check Results
 
-  ✓ no-new-cycles         — no new cycles introduced
-  ✗ max-complexity (30)   — 3 functions exceed threshold:
-      buildGraph (cognitive=495)  src/builder.js:335
-      extractJavaSymbols (cognitive=208)  src/extractors/java.js
-      extractSymbolsWalk (cognitive=197)  src/extractors/javascript.js
+  Changed files: 4  New files: 1  Deleted files: 0
 
-  Result: FAIL (exit code 1)
+  [PASS] cycles
+
+  1 predicates | 1 passed | 0 failed
 ```
 
 ```bash
-codegraph check --staged --max-blast-radius 50
+codegraph check --staged --blast-radius 50
 ```
 
 ```
 # Check Results
 
-  ✓ max-blast-radius (50) — max blast radius is 1
+  Changed files: 4  New files: 1  Deleted files: 0
 
-  Result: PASS (exit code 0)
+  [FAIL] blast-radius
+         buildGraph (function) at src/builder.js:335 — 67 callers (max: 50)
+
+  1 predicates | 0 passed | 1 failed
 ```
 
 ```bash
-codegraph check --no-boundary-violations -T
+codegraph check --staged --boundaries -T
 ```
 
 ```
 # Check Results
 
-  ✓ no-boundary-violations — no architecture boundary violations
+  Changed files: 4  New files: 1  Deleted files: 0
+
+  [PASS] boundaries
 
-  Result: PASS (exit code 0)
+  1 predicates | 1 passed | 0 failed
 ```
 
 ---

docs/examples/MCP.md

@@ -946,36 +946,37 @@ Configurable pass/fail gates. Returns structured results with exit status.
 ```json
 {
   "tool": "check",
-  "arguments": { "staged": true, "no_new_cycles": true, "max_complexity": 30 }
+  "arguments": { "staged": true, "cycles": true, "blast_radius": 50 }
 }
 ```
 
 ```json
 {
-  "checks": [
-    { "name": "no-new-cycles", "passed": true, "detail": "no new cycles introduced" },
-    { "name": "max-complexity", "passed": false, "threshold": 30, "violations": [
-      { "name": "buildGraph", "file": "src/builder.js", "line": 335, "cognitive": 495 },
-      { "name": "extractJavaSymbols", "file": "src/extractors/java.js", "cognitive": 208 }
+  "predicates": [
+    { "name": "cycles", "passed": true },
+    { "name": "blast-radius", "passed": false, "threshold": 50, "violations": [
+      { "name": "buildGraph", "kind": "function", "file": "src/builder.js", "line": 335, "transitiveCallers": 67 }
     ]}
   ],
+  "summary": { "changedFiles": 4, "newFiles": 1, "deletedFiles": 0, "total": 2, "passed": 1, "failed": 1 },
   "passed": false
 }
 ```
 
 ```json
 {
   "tool": "check",
-  "arguments": { "staged": true, "max_blast_radius": 50, "no_boundary_violations": true }
+  "arguments": { "staged": true, "boundaries": true, "signatures": true }
 }
 ```
 
 ```json
 {
-  "checks": [
-    { "name": "max-blast-radius", "passed": true, "detail": "max blast radius is 1" },
-    { "name": "no-boundary-violations", "passed": true, "detail": "no violations" }
+  "predicates": [
+    { "name": "boundaries", "passed": true },
+    { "name": "signatures", "passed": true }
   ],
+  "summary": { "changedFiles": 4, "newFiles": 1, "deletedFiles": 0, "total": 2, "passed": 2, "failed": 0 },
   "passed": true
 }
 ```

docs/guides/ai-agent-guide.md

@@ -441,14 +441,14 @@ codegraph batch target1 target2 target3 -T --json
 Configurable pass/fail gates with exit code 0 (pass) or 1 (fail).
 
 ```bash
-codegraph check --staged --no-new-cycles --max-complexity 30
-codegraph check --staged --max-blast-radius 50 --no-boundary-violations
+codegraph check --staged --cycles
+codegraph check --staged --blast-radius 50 --boundaries --signatures
 ```
 
 | | |
 |---|---|
 | **MCP tool** | `check` |
-| **Key flags** | `--staged`, `--no-new-cycles`, `--max-complexity <n>`, `--max-blast-radius <n>`, `--no-boundary-violations`, `-T` (no tests) |
+| **Key flags** | `--staged`, `--cycles`, `--blast-radius <n>`, `--boundaries`, `--signatures`, `-T` (no tests) |
 | **When to use** | CI gates, state machines, rollback triggers — anywhere you need a pass/fail signal |
 | **Output** | Per-predicate pass/fail results; exit code 0 or 1 |
 
@@ -894,7 +894,7 @@ This project uses codegraph for dependency analysis. The graph is at `.codegraph
 - `codegraph diff-impact main -T` — impact of branch vs main
 - `codegraph audit <target> -T` — structural summary + impact + health in one report
 - `codegraph triage -T` — ranked audit priority queue
-- `codegraph check --staged --no-new-cycles` — CI validation predicates (exit 0/1)
+- `codegraph check --staged --cycles` — CI validation predicates (exit 0/1)
 - `codegraph batch t1 t2 t3 -T --json` — batch query multiple targets
 
 ### Overview
@@ -1087,7 +1087,7 @@ fi
 | Get a full risk report for a function | `codegraph audit <name> -T` |
 | Get a ranked list of riskiest functions | `codegraph triage -T --limit 20` |
 | Batch query multiple targets at once | `codegraph batch t1 t2 t3 -T --json` |
-| Validate staged changes pass CI rules | `codegraph check --staged --no-new-cycles` |
+| Validate staged changes pass CI rules | `codegraph check --staged --cycles` |
 | Find who owns a piece of code | `codegraph owners <target>` |
 | Checkpoint the graph before refactoring | `codegraph snapshot save <name>` |
 | Restore graph after failed refactoring | `codegraph snapshot restore <name>` |

docs/roadmap/BACKLOG.md

@@ -55,7 +55,7 @@ Non-breaking, ordered by problem-fit:
 | 18 | ~~CODEOWNERS integration~~ | ~~Map graph nodes to CODEOWNERS entries. Show who owns each function, surface ownership boundaries in `diff-impact`. Inspired by CKB.~~ | Developer Experience | ~~`diff-impact` tells agents which teams to notify; ownership-aware impact analysis reduces missed reviews~~ | ✓ | ✓ | 3 | No | — | **DONE** — `src/owners.js` module with CODEOWNERS parser, matcher, and data functions. `codegraph owners [target]` CLI command with `--owner`, `--boundary`, `-f`, `-k`, `-T`, `-j` options. `code_owners` MCP tool. Integrated into `diff-impact` (affected owners + suggested reviewers). No new deps — glob patterns via ~30-line `patternToRegex`. PR #195. |
 | 22 | ~~Manifesto-driven pass/fail~~ | ~~User-defined rule engine with custom thresholds (e.g. "cognitive > 15 = fail", "cyclomatic > 10 = fail", "imports > 10 = decompose"). Outputs pass/fail per function/file. Generalizes ID 13 (boundary rules) into a generic rule system.~~ | Analysis | ~~Enables autonomous multi-agent audit workflows (GAUNTLET pattern); CI integration for code health gates with configurable thresholds~~ | ✓ | ✓ | 3 | No | — | **DONE** — `codegraph manifesto` with 9 configurable rules (cognitive, cyclomatic, nesting, MI, Halstead volume/effort/bugs, fan-in, fan-out). Warn/fail thresholds via `.codegraphrc.json`. Exit code 1 on any fail-level breach — CI gate ready. PR #138. |
 | 31 | ~~Graph snapshots~~ | ~~`codegraph snapshot save <name>` / `codegraph snapshot restore <name>` for lightweight SQLite DB backup and restore. Enables orchestrators to checkpoint before refactoring passes and instantly rollback without rebuilding. After Phase 4, also preserves embeddings and semantic metadata. Inspired by [Titan Paradigm](../docs/use-cases/titan-paradigm.md) STATE MACHINE phase.~~ | Orchestration | ~~Multi-agent workflows get instant rollback without re-running expensive builds or LLM calls — orchestrator checkpoints before each pass and restores on failure~~ | ✓ | ✓ | 3 | No | — | **DONE** — `codegraph snapshot` subcommand group with `save`, `restore`, `list`, `delete`. Uses SQLite `VACUUM INTO` for atomic, WAL-free snapshots in `.codegraph/snapshots/`. All 6 functions exported via programmatic API. PR #192. |
-| 30 | ~~Change validation predicates~~ | ~~`codegraph check --staged` with configurable predicates: `--no-new-cycles`, `--max-blast-radius N`, `--no-signature-changes`, `--no-boundary-violations`. Returns exit code 0/1 for CI gates and state machines. Inspired by [Titan Paradigm](../docs/use-cases/titan-paradigm.md) STATE MACHINE phase.~~ | CI | ~~Automated rollback triggers without parsing JSON — orchestrators and CI pipelines get first-class pass/fail signals for blast radius, cycles, and contract changes~~ | ✓ | ✓ | 3 | No | — | **DONE** — `codegraph check` with `--no-new-cycles`, `--max-complexity N`, `--max-blast-radius N`, `--no-boundary-violations`, and `--staged`/ref support. Exit code 0/1 for CI gates. `check` MCP tool. PR #225 + #230. |
+| 30 | ~~Change validation predicates~~ | ~~`codegraph check --staged` with configurable predicates: `--no-new-cycles`, `--max-blast-radius N`, `--no-signature-changes`, `--no-boundary-violations`. Returns exit code 0/1 for CI gates and state machines. Inspired by [Titan Paradigm](../docs/use-cases/titan-paradigm.md) STATE MACHINE phase.~~ | CI | ~~Automated rollback triggers without parsing JSON — orchestrators and CI pipelines get first-class pass/fail signals for blast radius, cycles, and contract changes~~ | ✓ | ✓ | 3 | No | — | **DONE** — `codegraph check` with `--cycles`, `--blast-radius N`, `--boundaries`, `--signatures`, and `--staged`/ref support. Exit code 0/1 for CI gates. `check` MCP tool. PR #225 + #230. |
 | 6 | ~~Formal code health metrics~~ | ~~Cyclomatic complexity, Maintainability Index, and Halstead metrics per function — we already parse the AST, the data is there. Inspired by code-health-meter (published in ACM TOSEM 2025).~~ | Analysis | ~~Agents can prioritize refactoring targets; `hotspots` becomes richer with quantitative health scores per function~~ | ✓ | ✓ | 2 | No | — | **DONE** — `codegraph complexity` provides cognitive, cyclomatic, nesting depth, Halstead (volume, difficulty, effort, bugs), and Maintainability Index per function. `--health` for full Halstead view, `--sort mi` to rank by MI, `--above-threshold` for flagged functions. `function_complexity` DB table. `complexity` MCP tool. PR #130 + #139. |
 | 11 | ~~Community detection~~ | ~~Leiden/Louvain algorithm to discover natural module boundaries vs actual file organization. Reveals which symbols are tightly coupled and whether the directory structure matches. Inspired by axon, GitNexus, CodeGraphMCPServer.~~ | Intelligence | ~~Surfaces architectural drift — when directory structure no longer matches actual dependency clusters; guides refactoring~~ | ✓ | ✓ | 2 | No | — | **DONE** — `codegraph communities` with Louvain algorithm. File-level and `--functions` function-level detection. `--drift` for drift analysis (split/merge candidates). `--resolution` tunable. `communities` MCP tool. PR #133/#134. |
 | 21 | ~~Cognitive + cyclomatic complexity~~ | ~~Cognitive Complexity (SonarSource) as the primary readability metric — penalizes nesting, so it subsumes nesting depth analysis. Cyclomatic complexity (McCabe) as secondary testability metric. Both computed from existing tree-sitter AST in a single traversal. Cognitive > 15 or cyclomatic > 10 = flag for refactoring. Extends ID 6 with the two most actionable metrics.~~ | Analysis | ~~Agents can flag hard-to-understand and hard-to-test functions in one pass; cognitive complexity captures both decision complexity and nesting depth in a single score~~ | ✓ | ✓ | 2 | No | — | **DONE** — Subsumed by ID 6. `codegraph complexity` provides both cognitive and cyclomatic metrics (plus nesting depth, Halstead, MI) in a single command. PR #130. |