perf: eliminate WASM re-parse for native complexity + build optimizations (#140)

* fix: native complexity upsert supplies all 18 Halstead/MI columns

The native complexity shortcut was passing only 4 params to the upsert
statement which now expects 18 (added by the Halstead/MI migration).
This crashed at runtime for natively-parsed functions. Fill Halstead/LOC/MI
columns with zeros since native engine intentionally skips WASM AST.

Also adds #[napi(js_name = "maxNesting")] to ComplexityMetrics so Rust
exports camelCase directly, removing the snake_case fallback in parser.js
and complexity.js. Cleans up a duplicate assertion and fixes indentation
in go.rs.

Impact: 4 functions changed, 4 affected

* fix: make complexity rules report-only in manifesto engine

Complexity rules (cognitive, cyclomatic, maxNesting) now always report
warnings but never cause process.exit(1). This keeps codegraph focused
on dependency graph analysis rather than acting as a CI linter gate.

- Add reportOnly flag to function-level complexity RULE_DEFS
- Force fail: null in resolveRules() when reportOnly is set
- Remove fail key from complexity defaults in config.js
- Add integration test verifying user fail thresholds are ignored

Impact: 1 functions changed, 2 affected

* style: format manifesto.js per biome rules

Impact: 1 functions changed, 2 affected

---------

Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>

Author: carlos-alm

crates/codegraph-core/src/complexity.rs

@@ -323,14 +323,7 @@ mod tests {
         let m = compute_js(
             "function f(x) { if (x > 0) { return 1; } else if (x < 0) { return -1; } else { return 0; } }",
         );
-        assert_eq!(m.cognitive, 4); // +1 if, +1 else-if, +1 else (from else-if's else_clause), +1 else-if cognitive
-        // Wait, let me recalculate:
-        // if: cognitive +1 (nesting 0), cyclomatic +1
-        // else-if: cognitive +1, cyclomatic +1 (no nesting)
-        // else: cognitive +1
-        // Total cognitive = 3, cyclomatic = 1 + 1 + 1 = 3
-        // Hmm, the else clause wrapping the else-if doesn't add anything (it's detected as else-if wrapper)
-        // So: if (+1 cog, +1 cyc), else-if (+1 cog, +1 cyc), plain else (+1 cog)
+        // if (+1 cog, +1 cyc), else-if (+1 cog, +1 cyc), plain else (+1 cog)
         // cognitive = 3, cyclomatic = 3
         assert_eq!(m.cognitive, 3);
         assert_eq!(m.cyclomatic, 3);

crates/codegraph-core/src/extractors/go.rs

@@ -111,7 +111,7 @@ fn walk_node(node: &Node, source: &[u8], symbols: &mut FileSymbols) {
                                                     line: start_line(&member),
                                                     end_line: Some(end_line(&member)),
                                                     decorators: None,
-                                    complexity: None,
+                                                    complexity: None,
                                                 });
                                             }
                                         }

crates/codegraph-core/src/types.rs

@@ -6,6 +6,7 @@ use serde::{Deserialize, Serialize};
 pub struct ComplexityMetrics {
     pub cognitive: u32,
     pub cyclomatic: u32,
+    #[napi(js_name = "maxNesting")]
     pub max_nesting: u32,
 }
 

src/complexity.js

@@ -581,7 +581,21 @@ export async function buildComplexityMetrics(db, fileSymbols, rootDir, _engineOp
             row.id,
             def.complexity.cognitive,
             def.complexity.cyclomatic,
-            def.complexity.maxNesting ?? def.complexity.max_nesting ?? 0,
+            def.complexity.maxNesting ?? 0,
+            0,
+            0,
+            0, // loc, sloc, commentLines
+            0,
+            0,
+            0,
+            0, // halstead n1, n2, bigN1, bigN2
+            0,
+            0,
+            0, // vocabulary, length, volume
+            0,
+            0,
+            0, // difficulty, effort, bugs
+            0, // maintainabilityIndex
           );
           analyzed++;
           continue;

src/config.js

@@ -26,9 +26,9 @@ export const DEFAULTS = {
   ci: { failOnCycles: false, impactThreshold: null },
   manifesto: {
     rules: {
-      cognitive: { warn: 15, fail: null },
-      cyclomatic: { warn: 10, fail: null },
-      maxNesting: { warn: 4, fail: null },
+      cognitive: { warn: 15 },
+      cyclomatic: { warn: 10 },
+      maxNesting: { warn: 4 },
       maintainabilityIndex: { warn: 20, fail: null },
       importCount: { warn: null, fail: null },
       exportCount: { warn: null, fail: null },

src/manifesto.js

@@ -12,18 +12,26 @@ import { debug } from './logger.js';
  * defaults: { warn, fail } — null means disabled
  */
 export const RULE_DEFS = [
-  { name: 'cognitive', level: 'function', metric: 'cognitive', defaults: { warn: 15, fail: null } },
+  {
+    name: 'cognitive',
+    level: 'function',
+    metric: 'cognitive',
+    defaults: { warn: 15, fail: null },
+    reportOnly: true,
+  },
   {
     name: 'cyclomatic',
     level: 'function',
     metric: 'cyclomatic',
     defaults: { warn: 10, fail: null },
+    reportOnly: true,
   },
   {
     name: 'maxNesting',
     level: 'function',
     metric: 'max_nesting',
     defaults: { warn: 4, fail: null },
+    reportOnly: true,
   },
   {
     name: 'importCount',
@@ -67,7 +75,7 @@ function resolveRules(userRules) {
     const user = userRules?.[def.name];
     resolved[def.name] = {
       warn: user?.warn !== undefined ? user.warn : def.defaults.warn,
-      fail: user?.fail !== undefined ? user.fail : def.defaults.fail,
+      fail: def.reportOnly ? null : user?.fail !== undefined ? user.fail : def.defaults.fail,
     };
   }
   return resolved;

src/parser.js

@@ -136,7 +136,7 @@ function normalizeNativeSymbols(result) {
         ? {
             cognitive: d.complexity.cognitive,
             cyclomatic: d.complexity.cyclomatic,
-            maxNesting: d.complexity.maxNesting ?? d.complexity.max_nesting,
+            maxNesting: d.complexity.maxNesting,
           }
         : null,
     })),

tests/integration/manifesto.test.js

@@ -291,6 +291,54 @@ describe('manifestoData', () => {
     }
   });
 
+  test('reportOnly complexity rules ignore user-configured fail thresholds', () => {
+    const configDir = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-manifesto-reportonly-'));
+    fs.mkdirSync(path.join(configDir, '.codegraph'));
+    const roDbPath = path.join(configDir, '.codegraph', 'graph.db');
+
+    fs.copyFileSync(dbPath, roDbPath);
+
+    // User attempts to set fail thresholds on complexity rules
+    fs.writeFileSync(
+      path.join(configDir, '.codegraphrc.json'),
+      JSON.stringify({
+        manifesto: {
+          rules: {
+            cognitive: { warn: 15, fail: 5 },
+            cyclomatic: { warn: 10, fail: 3 },
+            maxNesting: { warn: 4, fail: 2 },
+          },
+        },
+      }),
+    );
+
+    const origCwd = process.cwd();
+    try {
+      process.chdir(configDir);
+      const data = manifestoData(roDbPath);
+
+      // fail thresholds should be forced to null (reportOnly)
+      for (const name of ['cognitive', 'cyclomatic', 'maxNesting']) {
+        const rule = data.rules.find((r) => r.name === name);
+        expect(rule.thresholds.fail).toBeNull();
+      }
+
+      // All violations should be warn-only, never fail
+      const complexityViolations = data.violations.filter(
+        (v) => v.rule === 'cognitive' || v.rule === 'cyclomatic' || v.rule === 'maxNesting',
+      );
+      for (const v of complexityViolations) {
+        expect(v.level).toBe('warn');
+      }
+
+      // Overall result should pass (no fail-level violations)
+      expect(data.passed).toBe(true);
+    } finally {
+      process.chdir(origCwd);
+      fs.rmSync(configDir, { recursive: true, force: true });
+    }
+  });
+
   test('noCycles rule with fail threshold sets passed=false', () => {
     const configDir = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-manifesto-fail-'));
     fs.mkdirSync(path.join(configDir, '.codegraph'));