From 8e22728a1e51f14baaec040f0ee6c8bdfad03549 Mon Sep 17 00:00:00 2001
From: carlos-alm <127798846+carlos-alm@users.noreply.github.com>
Date: Thu, 26 Mar 2026 01:48:56 -0600
Subject: [PATCH 1/4] fix: make WASM grammar build resilient to transient
 failures

The prepare script now treats build:wasm as non-fatal since the native
engine is the primary parser. Individual grammar build failures are
caught and warned instead of aborting the entire build.
---
 package.json          |  2 +-
 scripts/build-wasm.ts | 25 ++++++++++++++++++-------
 2 files changed, 19 insertions(+), 8 deletions(-)

diff --git a/package.json b/package.json
index af3a1442..a2d6bf9c 100644
--- a/package.json
+++ b/package.json
@@ -41,7 +41,7 @@
     "format": "biome format --write src/ tests/",
     "prepack": "npm run build",
     "clean": "node -e \"require('fs').rmSync('dist',{recursive:true,force:true});require('fs').rmSync('.tsbuildinfo',{force:true})\"",
-    "prepare": "npm run build:wasm && npm run build && husky && npm run deps:tree",
+    "prepare": "(npm run build:wasm || echo 'WARN: WASM grammar build failed (non-fatal — native engine available)') && npm run build && husky && npm run deps:tree",
     "deps:tree": "node scripts/node-ts.js scripts/gen-deps.ts",
     "benchmark": "node --experimental-strip-types --import ./scripts/ts-resolve-loader.js scripts/benchmark.ts",
     "release": "commit-and-tag-version",
diff --git a/scripts/build-wasm.ts b/scripts/build-wasm.ts
index 42d8c141..cc0268e9 100644
--- a/scripts/build-wasm.ts
+++ b/scripts/build-wasm.ts
@@ -36,17 +36,28 @@ const grammars = [
   { name: 'tree-sitter-php', pkg: 'tree-sitter-php', sub: 'php' },
 ];
 
+let failed = 0;
 for (const g of grammars) {
   const pkgDir = dirname(require.resolve(`${g.pkg}/package.json`));
   const grammarDir = g.sub ? resolve(pkgDir, g.sub) : pkgDir;
 
   console.log(`Building ${g.name}.wasm from ${grammarDir}...`);
-  execFileSync('npx', ['tree-sitter', 'build', '--wasm', grammarDir], {
-    cwd: grammarsDir,
-    stdio: 'inherit',
-    shell: true,
-  });
-  console.log(`  Done: ${g.name}.wasm`);
+  try {
+    execFileSync('npx', ['tree-sitter', 'build', '--wasm', grammarDir], {
+      cwd: grammarsDir,
+      stdio: 'inherit',
+      shell: true,
+    });
+    console.log(`  Done: ${g.name}.wasm`);
+  } catch (err: any) {
+    failed++;
+    console.warn(`  WARN: Failed to build ${g.name}.wasm — ${err.message ?? 'unknown error'}`);
+  }
 }
 
-console.log('\nAll grammars built successfully into grammars/');
+if (failed > 0) {
+  console.warn(`\n${failed}/${grammars.length} grammars failed to build (non-fatal — native engine available)`);
+  process.exitCode = 1;
+} else {
+  console.log('\nAll grammars built successfully into grammars/');
+}

From 637a87377f35a84e219a9cfc86bd26bb48933a72 Mon Sep 17 00:00:00 2001
From: carlos-alm <127798846+carlos-alm@users.noreply.github.com>
Date: Thu, 26 Mar 2026 01:54:34 -0600
Subject: [PATCH 2/4] fix(lint): disable noNonNullAssertion and noExplicitAny
 rules, clean up suppressions
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

These rules produce hundreds of warnings from the JS→TS migration (Phase 6)
and are not actionable yet. Auto-fixed useLiteralKeys and noUnusedImports,
removed 69 now-unnecessary biome-ignore comments, and deleted one unused
interface.
---
 biome.json                                    |   8 +-
 src/ast-analysis/engine.ts                    |   3 -
 src/ast-analysis/shared.ts                    |   1 -
 src/ast-analysis/visitors/cfg-shared.ts       |   1 -
 .../visitors/complexity-visitor.ts            |   1 -
 src/ast-analysis/visitors/dataflow-visitor.ts |   1 -
 src/cli/commands/branch-compare.ts            |   2 +-
 src/cli/commands/build.ts                     |   2 +-
 src/cli/commands/info.ts                      |   2 +-
 src/cli/commands/watch.ts                     |   2 +-
 src/cli/index.ts                              |   4 +-
 src/cli/types.ts                              |   2 +-
 src/domain/analysis/brief.ts                  |   1 -
 src/domain/analysis/context.ts                |   8 +-
 src/domain/analysis/diff-impact.ts            |   2 -
 src/domain/analysis/exports.ts                |   2 -
 src/domain/analysis/fn-impact.ts              |   1 -
 src/domain/analysis/module-map.ts             |   6 +-
 .../graph/builder/stages/build-edges.ts       |   1 -
 .../graph/builder/stages/detect-changes.ts    |  14 +--
 src/domain/graph/cycles.ts                    |   4 +-
 src/domain/graph/resolve.ts                   |   2 -
 src/domain/parser.ts                          |   8 --
 src/extractors/javascript.ts                  | 115 +++++++++--------
 src/features/audit.ts                         |   3 +-
 src/features/cochange.ts                      |   8 +-
 src/features/communities.ts                   |   8 +-
 src/features/complexity-query.ts              |   1 -
 src/features/complexity.ts                    |   1 -
 src/features/dataflow.ts                      | 118 +++++++-----------
 src/features/flow.ts                          |   1 -
 src/features/graph-enrichment.ts              |   4 +-
 src/features/manifesto.ts                     |  16 +--
 src/features/snapshot.ts                      |   1 -
 src/features/triage.ts                        |   4 +-
 src/graph/algorithms/leiden/adapter.ts        |   2 +-
 src/infrastructure/config.ts                  |   8 +-
 src/infrastructure/registry.ts                |   2 +-
 src/infrastructure/update-check.ts            |   6 +-
 src/mcp/server.ts                             |   6 -
 src/mcp/tools/audit.ts                        |   2 +-
 src/mcp/tools/cfg.ts                          |   2 +-
 src/mcp/tools/check.ts                        |   4 +-
 src/mcp/tools/dataflow.ts                     |   4 +-
 src/mcp/tools/export-graph.ts                 |   2 +-
 src/mcp/tools/index.ts                        |   1 -
 src/mcp/tools/query.ts                        |   2 +-
 src/mcp/tools/semantic-search.ts              |   2 +-
 src/mcp/tools/sequence.ts                     |   2 +-
 src/mcp/tools/symbol-children.ts              |   2 +-
 src/mcp/tools/triage.ts                       |   2 +-
 src/presentation/audit.ts                     |   1 -
 src/presentation/diff-impact-mermaid.ts       |   2 -
 src/presentation/flow.ts                      |   2 -
 src/presentation/manifesto.ts                 |   1 -
 src/presentation/queries-cli/inspect.ts       |   1 -
 src/presentation/result-formatter.ts          |   1 -
 src/presentation/sequence.ts                  |   1 -
 src/presentation/structure.ts                 |  12 --
 src/presentation/triage.ts                    |   1 -
 src/types.ts                                  |  10 +-
 src/vendor.d.ts                               |   1 -
 62 files changed, 171 insertions(+), 269 deletions(-)

diff --git a/biome.json b/biome.json
index a64e090c..688f8ddb 100644
--- a/biome.json
+++ b/biome.json
@@ -10,7 +10,13 @@
   },
   "linter": {
     "rules": {
-      "recommended": true
+      "recommended": true,
+      "style": {
+        "noNonNullAssertion": "off"
+      },
+      "suspicious": {
+        "noExplicitAny": "off"
+      }
     }
   },
   "javascript": {
diff --git a/src/ast-analysis/engine.ts b/src/ast-analysis/engine.ts
index a717cf59..fe0b609e 100644
--- a/src/ast-analysis/engine.ts
+++ b/src/ast-analysis/engine.ts
@@ -219,7 +219,6 @@ function setupVisitors(
       walkerOpts.getFunctionName = (node: TreeSitterNode): string | null => {
         const nameNode = node.childForFieldName('name');
         if (nameNode) return nameNode.text;
-        // biome-ignore lint/suspicious/noExplicitAny: DataflowRulesConfig is structurally compatible at runtime
         if (dfRules) return getFuncName(node, dfRules as any);
         return null;
       };
@@ -362,7 +361,6 @@ async function delegateToBuildFunctions(
     const t0 = performance.now();
     try {
       const { buildAstNodes } = await import('../features/ast.js');
-      // biome-ignore lint/suspicious/noExplicitAny: ExtractorOutput is a superset of the local FileSymbols expected by buildAstNodes
       await buildAstNodes(db, fileSymbols as Map<string, any>, rootDir, engineOpts);
     } catch (err: unknown) {
       debug(`buildAstNodes failed: ${(err as Error).message}`);
@@ -374,7 +372,6 @@ async function delegateToBuildFunctions(
     const t0 = performance.now();
     try {
       const { buildComplexityMetrics } = await import('../features/complexity.js');
-      // biome-ignore lint/suspicious/noExplicitAny: ExtractorOutput is a superset of the local FileSymbols expected by buildComplexityMetrics
       await buildComplexityMetrics(db, fileSymbols as Map<string, any>, rootDir, engineOpts);
     } catch (err: unknown) {
       debug(`buildComplexityMetrics failed: ${(err as Error).message}`);
diff --git a/src/ast-analysis/shared.ts b/src/ast-analysis/shared.ts
index 18b197db..a427a2d2 100644
--- a/src/ast-analysis/shared.ts
+++ b/src/ast-analysis/shared.ts
@@ -176,7 +176,6 @@ export function findFunctionNode(
     }
 
     for (let i = 0; i < node.childCount; i++) {
-      // biome-ignore lint/style/noNonNullAssertion: tree-sitter child(i) within childCount is always non-null
       search(node.child(i)!);
     }
   }
diff --git a/src/ast-analysis/visitors/cfg-shared.ts b/src/ast-analysis/visitors/cfg-shared.ts
index be0066df..9987918e 100644
--- a/src/ast-analysis/visitors/cfg-shared.ts
+++ b/src/ast-analysis/visitors/cfg-shared.ts
@@ -1,6 +1,5 @@
 import type { TreeSitterNode } from '../../types.js';
 
-// biome-ignore lint/suspicious/noExplicitAny: CFG rules are opaque language-specific objects
 export type AnyRules = any;
 
 /** Callback type for the mutual recursion with processStatements in cfg-visitor. */
diff --git a/src/ast-analysis/visitors/complexity-visitor.ts b/src/ast-analysis/visitors/complexity-visitor.ts
index de888622..ffbf47ab 100644
--- a/src/ast-analysis/visitors/complexity-visitor.ts
+++ b/src/ast-analysis/visitors/complexity-visitor.ts
@@ -5,7 +5,6 @@ import {
   computeMaintainabilityIndex,
 } from '../metrics.js';
 
-// biome-ignore lint/suspicious/noExplicitAny: complexity/halstead rules are opaque language-specific objects
 type AnyRules = any;
 
 interface ComplexityAcc {
diff --git a/src/ast-analysis/visitors/dataflow-visitor.ts b/src/ast-analysis/visitors/dataflow-visitor.ts
index 72ba64db..aac5dee3 100644
--- a/src/ast-analysis/visitors/dataflow-visitor.ts
+++ b/src/ast-analysis/visitors/dataflow-visitor.ts
@@ -10,7 +10,6 @@ import {
   truncate,
 } from '../visitor-utils.js';
 
-// biome-ignore lint/suspicious/noExplicitAny: dataflow rules are opaque language-specific objects
 type AnyRules = any;
 
 interface ScopeEntry {
diff --git a/src/cli/commands/branch-compare.ts b/src/cli/commands/branch-compare.ts
index fc72164f..9e7e0b14 100644
--- a/src/cli/commands/branch-compare.ts
+++ b/src/cli/commands/branch-compare.ts
@@ -13,7 +13,7 @@ export const command: CommandDefinition = {
   async execute([base, target], opts, ctx) {
     const { branchCompare } = await import('../../presentation/branch-compare.js');
     await branchCompare(base!, target!, {
-      engine: ctx.program.opts()['engine'],
+      engine: ctx.program.opts().engine,
       depth: parseInt(opts.depth as string, 10),
       noTests: ctx.resolveNoTests(opts),
       json: opts.json,
diff --git a/src/cli/commands/build.ts b/src/cli/commands/build.ts
index 143065e1..25b5d849 100644
--- a/src/cli/commands/build.ts
+++ b/src/cli/commands/build.ts
@@ -15,7 +15,7 @@ export const command: CommandDefinition = {
   ],
   async execute([dir], opts, ctx) {
     const root = path.resolve(dir || '.');
-    const engine = ctx.program.opts()['engine'];
+    const engine = ctx.program.opts().engine;
     await buildGraph(root, {
       incremental: opts.incremental as boolean,
       ast: opts.ast as boolean,
diff --git a/src/cli/commands/info.ts b/src/cli/commands/info.ts
index aa295754..e56ffca5 100644
--- a/src/cli/commands/info.ts
+++ b/src/cli/commands/info.ts
@@ -9,7 +9,7 @@ export const command: CommandDefinition = {
     );
     const { getActiveEngine } = await import('../../domain/parser.js');
 
-    const engine = ctx.program.opts()['engine'];
+    const engine = ctx.program.opts().engine;
     const { name: activeName, version: activeVersion } = getActiveEngine({ engine });
     const nativeAvailable = isNativeAvailable();
 
diff --git a/src/cli/commands/watch.ts b/src/cli/commands/watch.ts
index 5b3ef06d..90e5f706 100644
--- a/src/cli/commands/watch.ts
+++ b/src/cli/commands/watch.ts
@@ -7,7 +7,7 @@ export const command: CommandDefinition = {
   description: 'Watch project for file changes and incrementally update the graph',
   async execute([dir], _opts, ctx) {
     const root = path.resolve(dir || '.');
-    const engine = ctx.program.opts()['engine'];
+    const engine = ctx.program.opts().engine;
     await watchProject(root, { engine });
   },
 };
diff --git a/src/cli/index.ts b/src/cli/index.ts
index c4e9cc91..3bbca34a 100644
--- a/src/cli/index.ts
+++ b/src/cli/index.ts
@@ -27,12 +27,12 @@ program
   .option('--engine <engine>', 'Parser engine: native, wasm, or auto (default: auto)', 'auto')
   .hook('preAction', (thisCommand) => {
     const opts = thisCommand.opts();
-    if (opts['verbose']) setVerbose(true);
+    if (opts.verbose) setVerbose(true);
   })
   .hook('postAction', async (_thisCommand, actionCommand) => {
     const name = actionCommand.name();
     if (name === 'mcp' || name === 'watch') return;
-    if (actionCommand.opts()['json']) return;
+    if (actionCommand.opts().json) return;
     try {
       const result = await checkForUpdates(pkg.version);
       if (result) printUpdateNotification(result.current, result.latest);
diff --git a/src/cli/types.ts b/src/cli/types.ts
index b9d31e5c..cfe2e79c 100644
--- a/src/cli/types.ts
+++ b/src/cli/types.ts
@@ -27,7 +27,7 @@ export interface CommandDefinition {
   description: string;
   queryOpts?: boolean;
   options?: Array<[string, string, ...unknown[]]>;
-  validate?(args: string[], opts: CommandOpts, ctx: CliContext): string | void;
+  validate?(args: string[], opts: CommandOpts, ctx: CliContext): string | undefined;
   execute?(args: string[], opts: CommandOpts, ctx: CliContext): void | Promise<void>;
   subcommands?: CommandDefinition[];
 }
diff --git a/src/domain/analysis/brief.ts b/src/domain/analysis/brief.ts
index b02704c7..4fb330a9 100644
--- a/src/domain/analysis/brief.ts
+++ b/src/domain/analysis/brief.ts
@@ -113,7 +113,6 @@ function countTransitiveImporters(
 export function briefData(
   file: string,
   customDbPath: string,
-  // biome-ignore lint/suspicious/noExplicitAny: config shape is dynamic
   opts: { noTests?: boolean; config?: any } = {},
 ) {
   const db = openReadonlyOrFail(customDbPath);
diff --git a/src/domain/analysis/context.ts b/src/domain/analysis/context.ts
index 71bb2d19..9f3f42dd 100644
--- a/src/domain/analysis/context.ts
+++ b/src/domain/analysis/context.ts
@@ -379,7 +379,6 @@ function explainFunctionImpl(
   });
 }
 
-// biome-ignore lint/suspicious/noExplicitAny: explainFunctionImpl results have dynamic shape with _depth
 function explainCallees(
   parentResults: any[],
   currentDepth: number,
@@ -405,8 +404,8 @@ function explainCallees(
       );
       const exact = calleeResults.find((cr) => cr.file === callee.file && cr.line === callee.line);
       if (exact) {
-        (exact as Record<string, unknown>)['_depth'] =
-          (((r as Record<string, unknown>)['_depth'] as number) || 0) + 1;
+        (exact as Record<string, unknown>)._depth =
+          (((r as Record<string, unknown>)._depth as number) || 0) + 1;
         newCallees.push(exact);
       }
     }
@@ -431,7 +430,6 @@ export function contextData(
     kind?: string;
     limit?: number;
     offset?: number;
-    // biome-ignore lint/suspicious/noExplicitAny: config shape is dynamic
     config?: any;
   } = {},
 ) {
@@ -509,7 +507,6 @@ export function explainData(
     depth?: number;
     limit?: number;
     offset?: number;
-    // biome-ignore lint/suspicious/noExplicitAny: config shape is dynamic
     config?: any;
   } = {},
 ) {
@@ -533,7 +530,6 @@ export function explainData(
         : explainFunctionImpl(db, target, noTests, getFileLines, displayOpts);
 
     if (kind === 'function' && depth > 0 && results.length > 0) {
-      // biome-ignore lint/suspicious/noExplicitAny: results are function results when kind === 'function'
       const visited = new Set(results.map((r: any) => `${r.name}:${r.file}:${r.line ?? ''}`));
       explainCallees(results, depth, visited, db, noTests, getFileLines, displayOpts);
     }
diff --git a/src/domain/analysis/diff-impact.ts b/src/domain/analysis/diff-impact.ts
index 29b3c331..f1e2fc16 100644
--- a/src/domain/analysis/diff-impact.ts
+++ b/src/domain/analysis/diff-impact.ts
@@ -227,7 +227,6 @@ function checkBoundaryViolations(
   db: BetterSqlite3Database,
   changedRanges: Map<string, unknown>,
   noTests: boolean,
-  // biome-ignore lint/suspicious/noExplicitAny: opts shape varies by caller
   opts: any,
   repoRoot: string,
 ) {
@@ -266,7 +265,6 @@ export function diffImpactData(
     includeImplementors?: boolean;
     limit?: number;
     offset?: number;
-    // biome-ignore lint/suspicious/noExplicitAny: config shape is dynamic
     config?: any;
   } = {},
 ) {
diff --git a/src/domain/analysis/exports.ts b/src/domain/analysis/exports.ts
index 90d8a2ae..f0162e0e 100644
--- a/src/domain/analysis/exports.ts
+++ b/src/domain/analysis/exports.ts
@@ -34,7 +34,6 @@ export function exportsData(
     unused?: boolean;
     limit?: number;
     offset?: number;
-    // biome-ignore lint/suspicious/noExplicitAny: config shape is dynamic
     config?: any;
   } = {},
 ) {
@@ -84,7 +83,6 @@ export function exportsData(
       totalReexported: first.totalReexported,
       totalReexportedUnused: first.totalReexportedUnused,
     };
-    // biome-ignore lint/suspicious/noExplicitAny: paginateResult returns dynamic shape
     const paginated: any = paginateResult(base, 'results', {
       limit: opts.limit,
       offset: opts.offset,
diff --git a/src/domain/analysis/fn-impact.ts b/src/domain/analysis/fn-impact.ts
index 114b2db7..d4e47c3a 100644
--- a/src/domain/analysis/fn-impact.ts
+++ b/src/domain/analysis/fn-impact.ts
@@ -203,7 +203,6 @@ export function fnImpactData(
     includeImplementors?: boolean;
     limit?: number;
     offset?: number;
-    // biome-ignore lint/suspicious/noExplicitAny: config shape is dynamic
     config?: any;
   } = {},
 ) {
diff --git a/src/domain/analysis/module-map.ts b/src/domain/analysis/module-map.ts
index b2c3f8de..2a8c9c19 100644
--- a/src/domain/analysis/module-map.ts
+++ b/src/domain/analysis/module-map.ts
@@ -380,11 +380,7 @@ export function moduleMapData(customDbPath: string, limit = 20, opts: { noTests?
   }
 }
 
-export function statsData(
-  customDbPath: string,
-  // biome-ignore lint/suspicious/noExplicitAny: config shape is dynamic
-  opts: { noTests?: boolean; config?: any } = {},
-) {
+export function statsData(customDbPath: string, opts: { noTests?: boolean; config?: any } = {}) {
   const db = openReadonlyOrFail(customDbPath);
   try {
     const noTests = opts.noTests || false;
diff --git a/src/domain/graph/builder/stages/build-edges.ts b/src/domain/graph/builder/stages/build-edges.ts
index 70da56f4..a5878a1b 100644
--- a/src/domain/graph/builder/stages/build-edges.ts
+++ b/src/domain/graph/builder/stages/build-edges.ts
@@ -12,7 +12,6 @@ import { loadNative } from '../../../../infrastructure/native.js';
 import type {
   Call,
   ClassRelation,
-  Definition,
   ExtractorOutput,
   Import,
   NativeAddon,
diff --git a/src/domain/graph/builder/stages/detect-changes.ts b/src/domain/graph/builder/stages/detect-changes.ts
index cbb18897..f6a5b907 100644
--- a/src/domain/graph/builder/stages/detect-changes.ts
+++ b/src/domain/graph/builder/stages/detect-changes.ts
@@ -11,7 +11,7 @@ import type BetterSqlite3 from 'better-sqlite3';
 import { closeDb } from '../../../../db/index.js';
 import { debug, info } from '../../../../infrastructure/logger.js';
 import { normalizePath } from '../../../../shared/constants.js';
-import type { EngineOpts, ExtractorOutput } from '../../../../types.js';
+import type { ExtractorOutput } from '../../../../types.js';
 import { parseFilesAuto } from '../../../parser.js';
 import { readJournal, writeJournalHeader } from '../../journal.js';
 import type { PipelineContext } from '../context.js';
@@ -227,7 +227,7 @@ function mtimeAndHashTiers(
 async function runPendingAnalysis(ctx: PipelineContext): Promise<boolean> {
   const { db, opts, engineOpts, allFiles, rootDir } = ctx;
   const needsCfg =
-    (opts as Record<string, unknown>)['cfg'] !== false &&
+    (opts as Record<string, unknown>).cfg !== false &&
     (() => {
       try {
         return (
@@ -239,7 +239,7 @@ async function runPendingAnalysis(ctx: PipelineContext): Promise<boolean> {
       }
     })();
   const needsDataflow =
-    (opts as Record<string, unknown>)['dataflow'] !== false &&
+    (opts as Record<string, unknown>).dataflow !== false &&
     (() => {
       try {
         return (
@@ -255,7 +255,7 @@ async function runPendingAnalysis(ctx: PipelineContext): Promise<boolean> {
   info('No file changes. Running pending analysis pass...');
   const analysisOpts = {
     ...engineOpts,
-    dataflow: needsDataflow && (opts as Record<string, unknown>)['dataflow'] !== false,
+    dataflow: needsDataflow && (opts as Record<string, unknown>).dataflow !== false,
   };
   const analysisSymbols: Map<string, ExtractorOutput> = await parseFilesAuto(
     allFiles,
@@ -359,7 +359,7 @@ function handleScopedBuild(ctx: PipelineContext): void {
     (item) => item.relPath || normalizePath(path.relative(rootDir, item.file)),
   );
   let reverseDeps = new Set<string>();
-  if (!(opts as Record<string, unknown>)['noReverseDeps']) {
+  if (!(opts as Record<string, unknown>).noReverseDeps) {
     const changedRelPaths = new Set<string>([...changePaths, ...ctx.removed]);
     reverseDeps = findReverseDependencies(db, changedRelPaths, rootDir);
   }
@@ -386,7 +386,7 @@ function handleIncrementalBuild(ctx: PipelineContext): void {
   const { db, rootDir, opts } = ctx;
   ctx.hasEmbeddings = detectHasEmbeddings(db);
   let reverseDeps = new Set<string>();
-  if (!(opts as Record<string, unknown>)['noReverseDeps']) {
+  if (!(opts as Record<string, unknown>).noReverseDeps) {
     const changedRelPaths = new Set<string>();
     for (const item of ctx.parseChanges) {
       changedRelPaths.add(item.relPath || normalizePath(path.relative(rootDir, item.file)));
@@ -410,7 +410,7 @@ function handleIncrementalBuild(ctx: PipelineContext): void {
 
 export async function detectChanges(ctx: PipelineContext): Promise<void> {
   const { db, allFiles, rootDir, incremental, forceFullRebuild, opts } = ctx;
-  if ((opts as Record<string, unknown>)['scope']) {
+  if ((opts as Record<string, unknown>).scope) {
     handleScopedBuild(ctx);
     return;
   }
diff --git a/src/domain/graph/cycles.ts b/src/domain/graph/cycles.ts
index 9517133d..88792a75 100644
--- a/src/domain/graph/cycles.ts
+++ b/src/domain/graph/cycles.ts
@@ -16,9 +16,9 @@ export function findCycles(
   const idToLabel = new Map<string, string>();
   for (const [id, attrs] of graph.nodes()) {
     if (fileLevel) {
-      idToLabel.set(id, attrs['file'] as string);
+      idToLabel.set(id, attrs.file as string);
     } else {
-      idToLabel.set(id, `${attrs['label']}|${attrs['file']}`);
+      idToLabel.set(id, `${attrs.label}|${attrs.file}`);
     }
   }
 
diff --git a/src/domain/graph/resolve.ts b/src/domain/graph/resolve.ts
index 8588c7c9..451b1e5b 100644
--- a/src/domain/graph/resolve.ts
+++ b/src/domain/graph/resolve.ts
@@ -8,7 +8,6 @@ import type { BareSpecifier, BatchResolvedMap, ImportBatchItem, PathAliases } fr
 // ── package.json exports resolution ─────────────────────────────────
 
 /** Cache: packageDir → parsed exports field (or null) */
-// biome-ignore lint/suspicious/noExplicitAny: package.json exports field has no fixed schema
 const _exportsCache: Map<string, any> = new Map();
 
 /**
@@ -56,7 +55,6 @@ function findPackageDir(packageName: string, rootDir: string): string | null {
  * Read and cache the exports field from a package's package.json.
  * Returns the exports value or null.
  */
-// biome-ignore lint/suspicious/noExplicitAny: package.json exports field has no fixed schema
 function getPackageExports(packageDir: string): any {
   if (_exportsCache.has(packageDir)) return _exportsCache.get(packageDir);
   try {
diff --git a/src/domain/parser.ts b/src/domain/parser.ts
index 0497d5e9..d8cb2325 100644
--- a/src/domain/parser.ts
+++ b/src/domain/parser.ts
@@ -69,7 +69,6 @@ interface ParseEngineOpts {
 
 interface ResolvedEngine {
   name: 'native' | 'wasm';
-  // biome-ignore lint/suspicious/noExplicitAny: native addon has no type declarations
   native: any;
 }
 
@@ -171,7 +170,6 @@ export function disposeParsers(): void {
   _queryCache.clear();
   if (_cachedLanguages) {
     for (const [id, lang] of _cachedLanguages) {
-      // biome-ignore lint/suspicious/noExplicitAny: .delete() exists at runtime on WASM Language objects but is missing from typings
       if (lang && typeof (lang as any).delete === 'function') {
         try {
           (lang as any).delete();
@@ -197,7 +195,6 @@ export function getParser(parsers: Map<string, Parser | null>, filePath: string)
  * don't each need to create parsers and re-parse independently.
  * Only parses files whose extension is in SUPPORTED_EXTENSIONS.
  */
-// biome-ignore lint/suspicious/noExplicitAny: fileSymbols values have dynamic shape from extractors
 export async function ensureWasmTrees(
   fileSymbols: Map<string, any>,
   rootDir: string,
@@ -274,7 +271,6 @@ function resolveEngine(opts: ParseEngineOpts = {}): ResolvedEngine {
  *  - Backward compat for older native binaries missing js_name annotations
  *  - dataflow argFlows/mutations bindingType -> binding wrapper
  */
-// biome-ignore lint/suspicious/noExplicitAny: native addon result has no type declarations
 function patchNativeResult(r: any): ExtractorOutput {
   // lineCount: napi(js_name) emits "lineCount"; older binaries may emit "line_count"
   r.lineCount = r.lineCount ?? r.line_count ?? null;
@@ -433,7 +429,6 @@ export const SUPPORTED_EXTENSIONS: Set<string> = new Set(_extToLang.keys());
  * matches inside comments and string literals.
  * TODO: Remove once all published native binaries include typeMap extraction (>= 3.2.0)
  */
-// biome-ignore lint/suspicious/noExplicitAny: return shape matches native result typeMap
 async function backfillTypeMap(
   filePath: string,
   source?: string,
@@ -491,7 +486,6 @@ function wasmExtractSymbols(
   if (!entry) return null;
   const query = _queryCache.get(entry.id) ?? undefined;
   // Query (web-tree-sitter) is structurally compatible with TreeSitterQuery at runtime
-  // biome-ignore lint/suspicious/noExplicitAny: thin WASM wrapper type mismatch
   const symbols = entry.extractor(tree as any, filePath, query as any);
   return symbols ? { symbols, tree, langId: entry.id } : null;
 }
@@ -643,7 +637,6 @@ export function getActiveEngine(opts: ParseEngineOpts = {}): {
  * Create a native ParseTreeCache for incremental parsing.
  * Returns null if the native engine is unavailable (WASM fallback).
  */
-// biome-ignore lint/suspicious/noExplicitAny: native ParseTreeCache has no type declarations
 export function createParseTreeCache(): any {
   const native = loadNative();
   if (!native || !native.ParseTreeCache) return null;
@@ -653,7 +646,6 @@ export function createParseTreeCache(): any {
 /**
  * Parse a file incrementally using the cache, or fall back to full parse.
  */
-// biome-ignore lint/suspicious/noExplicitAny: cache is native ParseTreeCache with no type declarations
 export async function parseFileIncremental(
   cache: any,
   filePath: string,
diff --git a/src/extractors/javascript.ts b/src/extractors/javascript.ts
index e6fa4fe1..ef88a6c2 100644
--- a/src/extractors/javascript.ts
+++ b/src/extractors/javascript.ts
@@ -102,44 +102,42 @@ function extractSymbolsQuery(tree: TreeSitterTree, query: TreeSitterQuery): Extr
     const c: Record<string, TreeSitterNode> = Object.create(null);
     for (const cap of match.captures) c[cap.name] = cap.node;
 
-    if (c['fn_node']) {
+    if (c.fn_node) {
       // function_declaration
-      const fnChildren = extractParameters(c['fn_node']);
+      const fnChildren = extractParameters(c.fn_node);
       definitions.push({
-        name: c['fn_name']!.text,
+        name: c.fn_name!.text,
         kind: 'function',
-        line: c['fn_node'].startPosition.row + 1,
-        endLine: nodeEndLine(c['fn_node']),
+        line: c.fn_node.startPosition.row + 1,
+        endLine: nodeEndLine(c.fn_node),
         children: fnChildren.length > 0 ? fnChildren : undefined,
       });
-    } else if (c['varfn_name']) {
+    } else if (c.varfn_name) {
       // variable_declarator with arrow_function / function_expression
-      const declNode = c['varfn_name'].parent?.parent;
-      const line = declNode
-        ? declNode.startPosition.row + 1
-        : c['varfn_name'].startPosition.row + 1;
-      const varFnChildren = extractParameters(c['varfn_value']!);
+      const declNode = c.varfn_name.parent?.parent;
+      const line = declNode ? declNode.startPosition.row + 1 : c.varfn_name.startPosition.row + 1;
+      const varFnChildren = extractParameters(c.varfn_value!);
       definitions.push({
-        name: c['varfn_name'].text,
+        name: c.varfn_name.text,
         kind: 'function',
         line,
-        endLine: nodeEndLine(c['varfn_value']!),
+        endLine: nodeEndLine(c.varfn_value!),
         children: varFnChildren.length > 0 ? varFnChildren : undefined,
       });
-    } else if (c['cls_node']) {
+    } else if (c.cls_node) {
       // class_declaration
-      const className = c['cls_name']!.text;
-      const startLine = c['cls_node'].startPosition.row + 1;
-      const clsChildren = extractClassProperties(c['cls_node']);
+      const className = c.cls_name!.text;
+      const startLine = c.cls_node.startPosition.row + 1;
+      const clsChildren = extractClassProperties(c.cls_node);
       definitions.push({
         name: className,
         kind: 'class',
         line: startLine,
-        endLine: nodeEndLine(c['cls_node']),
+        endLine: nodeEndLine(c.cls_node),
         children: clsChildren.length > 0 ? clsChildren : undefined,
       });
       const heritage =
-        c['cls_node'].childForFieldName('heritage') || findChild(c['cls_node'], 'class_heritage');
+        c.cls_node.childForFieldName('heritage') || findChild(c.cls_node, 'class_heritage');
       if (heritage) {
         const superName = extractSuperclass(heritage);
         if (superName) classes.push({ name: className, extends: superName, line: startLine });
@@ -148,58 +146,58 @@ function extractSymbolsQuery(tree: TreeSitterTree, query: TreeSitterQuery): Extr
           classes.push({ name: className, implements: iface, line: startLine });
         }
       }
-    } else if (c['meth_node']) {
+    } else if (c.meth_node) {
       // method_definition
-      const methName = c['meth_name']!.text;
-      const parentClass = findParentClass(c['meth_node']);
+      const methName = c.meth_name!.text;
+      const parentClass = findParentClass(c.meth_node);
       const fullName = parentClass ? `${parentClass}.${methName}` : methName;
-      const methChildren = extractParameters(c['meth_node']);
-      const methVis = extractVisibility(c['meth_node']);
+      const methChildren = extractParameters(c.meth_node);
+      const methVis = extractVisibility(c.meth_node);
       definitions.push({
         name: fullName,
         kind: 'method',
-        line: c['meth_node'].startPosition.row + 1,
-        endLine: nodeEndLine(c['meth_node']),
+        line: c.meth_node.startPosition.row + 1,
+        endLine: nodeEndLine(c.meth_node),
         children: methChildren.length > 0 ? methChildren : undefined,
         visibility: methVis,
       });
-    } else if (c['iface_node']) {
+    } else if (c.iface_node) {
       // interface_declaration (TS/TSX only)
-      const ifaceName = c['iface_name']!.text;
+      const ifaceName = c.iface_name!.text;
       definitions.push({
         name: ifaceName,
         kind: 'interface',
-        line: c['iface_node'].startPosition.row + 1,
-        endLine: nodeEndLine(c['iface_node']),
+        line: c.iface_node.startPosition.row + 1,
+        endLine: nodeEndLine(c.iface_node),
       });
       const body =
-        c['iface_node'].childForFieldName('body') ||
-        findChild(c['iface_node'], 'interface_body') ||
-        findChild(c['iface_node'], 'object_type');
+        c.iface_node.childForFieldName('body') ||
+        findChild(c.iface_node, 'interface_body') ||
+        findChild(c.iface_node, 'object_type');
       if (body) extractInterfaceMethods(body, ifaceName, definitions);
-    } else if (c['type_node']) {
+    } else if (c.type_node) {
       // type_alias_declaration (TS/TSX only)
       definitions.push({
-        name: c['type_name']!.text,
+        name: c.type_name!.text,
         kind: 'type',
-        line: c['type_node'].startPosition.row + 1,
-        endLine: nodeEndLine(c['type_node']),
+        line: c.type_node.startPosition.row + 1,
+        endLine: nodeEndLine(c.type_node),
       });
-    } else if (c['imp_node']) {
+    } else if (c.imp_node) {
       // import_statement
-      const isTypeOnly = c['imp_node'].text.startsWith('import type');
-      const modPath = c['imp_source']!.text.replace(/['"]/g, '');
-      const names = extractImportNames(c['imp_node']);
+      const isTypeOnly = c.imp_node.text.startsWith('import type');
+      const modPath = c.imp_source!.text.replace(/['"]/g, '');
+      const names = extractImportNames(c.imp_node);
       imports.push({
         source: modPath,
         names,
-        line: c['imp_node'].startPosition.row + 1,
+        line: c.imp_node.startPosition.row + 1,
         typeOnly: isTypeOnly,
       });
-    } else if (c['exp_node']) {
+    } else if (c.exp_node) {
       // export_statement
-      const exportLine = c['exp_node'].startPosition.row + 1;
-      const decl = c['exp_node'].childForFieldName('declaration');
+      const exportLine = c.exp_node.startPosition.row + 1;
+      const decl = c.exp_node.childForFieldName('declaration');
       if (decl) {
         const declType = decl.type;
         const kindMap: Record<string, string> = {
@@ -214,12 +212,11 @@ function extractSymbolsQuery(tree: TreeSitterTree, query: TreeSitterQuery): Extr
           if (n) exps.push({ name: n.text, kind: kind as Export['kind'], line: exportLine });
         }
       }
-      const source =
-        c['exp_node'].childForFieldName('source') || findChild(c['exp_node'], 'string');
+      const source = c.exp_node.childForFieldName('source') || findChild(c.exp_node, 'string');
       if (source && !decl) {
         const modPath = source.text.replace(/['"]/g, '');
-        const reexportNames = extractImportNames(c['exp_node']);
-        const nodeText = c['exp_node'].text;
+        const reexportNames = extractImportNames(c.exp_node);
+        const nodeText = c.exp_node.text;
         const isWildcard = nodeText.includes('export *') || nodeText.includes('export*');
         imports.push({
           source: modPath,
@@ -229,25 +226,25 @@ function extractSymbolsQuery(tree: TreeSitterTree, query: TreeSitterQuery): Extr
           wildcardReexport: isWildcard && reexportNames.length === 0,
         });
       }
-    } else if (c['callfn_node']) {
+    } else if (c.callfn_node) {
       // call_expression with identifier function
       calls.push({
-        name: c['callfn_name']!.text,
-        line: c['callfn_node'].startPosition.row + 1,
+        name: c.callfn_name!.text,
+        line: c.callfn_node.startPosition.row + 1,
       });
-    } else if (c['callmem_node']) {
+    } else if (c.callmem_node) {
       // call_expression with member_expression function
-      const callInfo = extractCallInfo(c['callmem_fn']!, c['callmem_node']);
+      const callInfo = extractCallInfo(c.callmem_fn!, c.callmem_node);
       if (callInfo) calls.push(callInfo);
-      const cbDef = extractCallbackDefinition(c['callmem_node'], c['callmem_fn']);
+      const cbDef = extractCallbackDefinition(c.callmem_node, c.callmem_fn);
       if (cbDef) definitions.push(cbDef);
-    } else if (c['callsub_node']) {
+    } else if (c.callsub_node) {
       // call_expression with subscript_expression function
-      const callInfo = extractCallInfo(c['callsub_fn']!, c['callsub_node']);
+      const callInfo = extractCallInfo(c.callsub_fn!, c.callsub_node);
       if (callInfo) calls.push(callInfo);
-    } else if (c['assign_node']) {
+    } else if (c.assign_node) {
       // CommonJS: module.exports = require(...) / module.exports = { ...require(...) }
-      handleCommonJSAssignment(c['assign_left']!, c['assign_right']!, c['assign_node'], imports);
+      handleCommonJSAssignment(c.assign_left!, c.assign_right!, c.assign_node, imports);
     }
   }
 
diff --git a/src/features/audit.ts b/src/features/audit.ts
index 1acdf082..50d18a2c 100644
--- a/src/features/audit.ts
+++ b/src/features/audit.ts
@@ -30,7 +30,7 @@ function resolveThresholds(
         const repoRoot = path.resolve(dbDir, '..');
         return loadConfig(repoRoot);
       })();
-    const userRules = (cfg as Record<string, unknown>)['manifesto'] || {};
+    const userRules = (cfg as Record<string, unknown>).manifesto || {};
     const resolved: Record<string, ThresholdEntry> = {};
     for (const def of FUNCTION_RULES) {
       const user = (userRules as Record<string, { warn?: number; fail?: number }>)[def.name];
@@ -163,7 +163,6 @@ export function auditData(
   const explained = explainData(target, customDbPath, { noTests, depth: 0 });
 
   // Apply --file and --kind filters for function targets
-  // biome-ignore lint/suspicious/noExplicitAny: explainData returns a union type that varies by kind
   let results: any[] = explained.results;
   if (explained.kind === 'function') {
     if (fileFilters.length > 0)
diff --git a/src/features/cochange.ts b/src/features/cochange.ts
index 36b8d80b..ffda28d2 100644
--- a/src/features/cochange.ts
+++ b/src/features/cochange.ts
@@ -472,10 +472,10 @@ function getCoChangeMeta(db: BetterSqlite3Database): CoChangeMeta | null {
       meta[row.key] = row.value;
     }
     return {
-      analyzedAt: meta['analyzed_at'] || null,
-      since: meta['since'] || null,
-      minSupport: meta['min_support'] ? parseInt(meta['min_support'], 10) : null,
-      lastCommit: meta['last_analyzed_commit'] || null,
+      analyzedAt: meta.analyzed_at || null,
+      since: meta.since || null,
+      minSupport: meta.min_support ? parseInt(meta.min_support, 10) : null,
+      lastCommit: meta.last_analyzed_commit || null,
     };
   } catch {
     return null;
diff --git a/src/features/communities.ts b/src/features/communities.ts
index dbea6bfa..ce4cb9ae 100644
--- a/src/features/communities.ts
+++ b/src/features/communities.ts
@@ -50,12 +50,12 @@ function buildCommunityObjects(
     const memberData: CommunityMember[] = [];
     for (const key of members) {
       const attrs = graph.getNodeAttrs(key)!;
-      const dir = getDirectory(attrs['file'] as string);
+      const dir = getDirectory(attrs.file as string);
       dirCounts[dir] = (dirCounts[dir] || 0) + 1;
       memberData.push({
-        name: attrs['label'] as string,
-        file: attrs['file'] as string,
-        ...(attrs['kind'] ? { kind: attrs['kind'] as string } : {}),
+        name: attrs.label as string,
+        file: attrs.file as string,
+        ...(attrs.kind ? { kind: attrs.kind as string } : {}),
       });
     }
 
diff --git a/src/features/complexity-query.ts b/src/features/complexity-query.ts
index 58de031d..e494b6b2 100644
--- a/src/features/complexity-query.ts
+++ b/src/features/complexity-query.ts
@@ -58,7 +58,6 @@ export function complexityData(
 
     // Load thresholds from config
     const config = opts.config || loadConfig(process.cwd());
-    // biome-ignore lint/suspicious/noExplicitAny: thresholds come from config with dynamic keys
     const thresholds: any = config.manifesto?.rules || {
       cognitive: { warn: 15, fail: null },
       cyclomatic: { warn: 10, fail: null },
diff --git a/src/features/complexity.ts b/src/features/complexity.ts
index b83acfaf..bd4a27b0 100644
--- a/src/features/complexity.ts
+++ b/src/features/complexity.ts
@@ -383,7 +383,6 @@ function getTreeForFile(
   rootDir: string,
   parsers: unknown,
   extToLang: Map<string, string> | null,
-  // biome-ignore lint/suspicious/noExplicitAny: dynamic import from parser.js
   getParser: (parsers: any, absPath: string) => any,
 ): { tree: { rootNode: TreeSitterNode }; langId: string } | null {
   let tree = symbols._tree;
diff --git a/src/features/dataflow.ts b/src/features/dataflow.ts
index ab5ae728..8315b524 100644
--- a/src/features/dataflow.ts
+++ b/src/features/dataflow.ts
@@ -65,7 +65,7 @@ export function extractDataflow(
     getFunctionName: () => null, // dataflow visitor handles its own name extraction
   });
 
-  return results['dataflow'] as DataflowResult;
+  return results.dataflow as DataflowResult;
 }
 
 // ── Build-Time Helpers ──────────────────────────────────────────────────────
@@ -79,7 +79,6 @@ interface FileSymbolsDataflow {
 
 async function initDataflowParsers(
   fileSymbols: Map<string, FileSymbolsDataflow>,
-  // biome-ignore lint/suspicious/noExplicitAny: dynamic import from parser.js
 ): Promise<{ parsers: unknown; getParserFn: ((parsers: any, absPath: string) => any) | null }> {
   let needsFallback = false;
 
@@ -94,7 +93,6 @@ async function initDataflowParsers(
   }
 
   let parsers: unknown = null;
-  // biome-ignore lint/suspicious/noExplicitAny: dynamic import from parser.js
   let getParserFn: ((parsers: any, absPath: string) => any) | null = null;
 
   if (needsFallback) {
@@ -113,7 +111,6 @@ function getDataflowForFile(
   rootDir: string,
   extToLang: Map<string, string>,
   parsers: unknown,
-  // biome-ignore lint/suspicious/noExplicitAny: dynamic import from parser.js
   getParserFn: ((parsers: any, absPath: string) => any) | null,
 ): DataflowResult | null {
   if (symbols.dataflow) return symbols.dataflow;
@@ -369,74 +366,55 @@ export function dataflowData(
     const results = nodes.map((node: NodeRow) => {
       const sym = normalizeSymbol(node, db, hc);
 
-      const flowsTo = flowsToOut.all(node.id).map(
-        // biome-ignore lint/suspicious/noExplicitAny: raw DB row
-        (r: any) => ({
-          target: r.target_name,
-          kind: r.target_kind,
-          file: r.target_file,
-          line: r.line,
-          paramIndex: r.param_index,
-          expression: r.expression,
-          confidence: r.confidence,
-        }),
-      );
-
-      const flowsFrom = flowsToIn.all(node.id).map(
-        // biome-ignore lint/suspicious/noExplicitAny: raw DB row
-        (r: any) => ({
-          source: r.source_name,
-          kind: r.source_kind,
-          file: r.source_file,
-          line: r.line,
-          paramIndex: r.param_index,
-          expression: r.expression,
-          confidence: r.confidence,
-        }),
-      );
-
-      const returnConsumers = returnsOut.all(node.id).map(
-        // biome-ignore lint/suspicious/noExplicitAny: raw DB row
-        (r: any) => ({
-          consumer: r.target_name,
-          kind: r.target_kind,
-          file: r.target_file,
-          line: r.line,
-          expression: r.expression,
-        }),
-      );
-
-      const returnedBy = returnsIn.all(node.id).map(
-        // biome-ignore lint/suspicious/noExplicitAny: raw DB row
-        (r: any) => ({
-          producer: r.source_name,
-          kind: r.source_kind,
-          file: r.source_file,
-          line: r.line,
-          expression: r.expression,
-        }),
-      );
-
-      const mutatesTargets = mutatesOut.all(node.id).map(
-        // biome-ignore lint/suspicious/noExplicitAny: raw DB row
-        (r: any) => ({
-          target: r.target_name,
-          expression: r.expression,
-          line: r.line,
-        }),
-      );
-
-      const mutatedBy = mutatesIn.all(node.id).map(
-        // biome-ignore lint/suspicious/noExplicitAny: raw DB row
-        (r: any) => ({
-          source: r.source_name,
-          expression: r.expression,
-          line: r.line,
-        }),
-      );
+      const flowsTo = flowsToOut.all(node.id).map((r: any) => ({
+        target: r.target_name,
+        kind: r.target_kind,
+        file: r.target_file,
+        line: r.line,
+        paramIndex: r.param_index,
+        expression: r.expression,
+        confidence: r.confidence,
+      }));
+
+      const flowsFrom = flowsToIn.all(node.id).map((r: any) => ({
+        source: r.source_name,
+        kind: r.source_kind,
+        file: r.source_file,
+        line: r.line,
+        paramIndex: r.param_index,
+        expression: r.expression,
+        confidence: r.confidence,
+      }));
+
+      const returnConsumers = returnsOut.all(node.id).map((r: any) => ({
+        consumer: r.target_name,
+        kind: r.target_kind,
+        file: r.target_file,
+        line: r.line,
+        expression: r.expression,
+      }));
+
+      const returnedBy = returnsIn.all(node.id).map((r: any) => ({
+        producer: r.source_name,
+        kind: r.source_kind,
+        file: r.source_file,
+        line: r.line,
+        expression: r.expression,
+      }));
+
+      const mutatesTargets = mutatesOut.all(node.id).map((r: any) => ({
+        target: r.target_name,
+        expression: r.expression,
+        line: r.line,
+      }));
+
+      const mutatedBy = mutatesIn.all(node.id).map((r: any) => ({
+        source: r.source_name,
+        expression: r.expression,
+        line: r.line,
+      }));
 
       if (noTests) {
-        // biome-ignore lint/suspicious/noExplicitAny: raw DB row results
         const filter = (arr: any[]) => arr.filter((r: any) => !isTestFile(r.file));
         return {
           ...sym,
diff --git a/src/features/flow.ts b/src/features/flow.ts
index 9b538905..08b40118 100644
--- a/src/features/flow.ts
+++ b/src/features/flow.ts
@@ -9,7 +9,6 @@ import { openReadonlyOrFail } from '../db/index.js';
 import { CORE_SYMBOL_KINDS, findMatchingNodes } from '../domain/queries.js';
 import { isTestFile } from '../infrastructure/test-filter.js';
 import { paginateResult } from '../shared/paginate.js';
-import type { BetterSqlite3Database } from '../types.js';
 import { FRAMEWORK_ENTRY_PREFIXES } from './structure.js';
 
 export function entryPointType(name: string): 'route' | 'event' | 'command' | 'exported' | null {
diff --git a/src/features/graph-enrichment.ts b/src/features/graph-enrichment.ts
index ce0505e5..d1af5ad0 100644
--- a/src/features/graph-enrichment.ts
+++ b/src/features/graph-enrichment.ts
@@ -356,9 +356,7 @@ function prepareFileLevelData(
     const color: string =
       cfg.colorBy === 'community' && community !== null
         ? COMMUNITY_COLORS[community % COMMUNITY_COLORS.length] || '#ccc'
-        : cfg.nodeColors?.['file'] ||
-          (DEFAULT_NODE_COLORS as Record<string, string>)['file'] ||
-          '#ccc';
+        : cfg.nodeColors?.file || (DEFAULT_NODE_COLORS as Record<string, string>).file || '#ccc';
 
     return {
       id,
diff --git a/src/features/manifesto.ts b/src/features/manifesto.ts
index 71780f98..edf22bc0 100644
--- a/src/features/manifesto.ts
+++ b/src/features/manifesto.ts
@@ -220,9 +220,9 @@ function evaluateFunctionRules(
       const value = row[def.metric] as number | null;
       if (value == null) continue;
       const meta = {
-        name: row['name'] as string,
-        file: row['file'] as string,
-        line: row['line'] as number,
+        name: row.name as string,
+        file: row.file as string,
+        line: row.line as number,
       };
       const status = checkThreshold(def.name, rules[def.name]!, value, meta, violations);
       if (status !== 'pass') {
@@ -304,9 +304,9 @@ function evaluateFileRules(
       const value = row[def.metric] as number | null;
       if (value == null) continue;
       const meta = {
-        name: row['name'] as string,
-        file: row['file'] as string,
-        line: row['line'] as number,
+        name: row.name as string,
+        file: row.file as string,
+        line: row.line as number,
       };
       const status = checkThreshold(def.name, rules[def.name]!, value, meta, violations);
       if (status !== 'pass') {
@@ -335,7 +335,7 @@ function evaluateGraphRules(
   violations: Violation[],
   ruleResults: RuleResult[],
 ): void {
-  const thresholds = rules['noCycles']!;
+  const thresholds = rules.noCycles!;
   if (!isEnabled(thresholds)) {
     ruleResults.push({
       name: 'noCycles',
@@ -393,7 +393,7 @@ function evaluateBoundaryRules(
   violations: Violation[],
   ruleResults: RuleResult[],
 ): void {
-  const thresholds = rules['boundaries']!;
+  const thresholds = rules.boundaries!;
   const boundaryConfig = config.manifesto?.boundaries;
 
   // Auto-enable at warn level when boundary config exists but threshold not set
diff --git a/src/features/snapshot.ts b/src/features/snapshot.ts
index ea09c2f8..117af067 100644
--- a/src/features/snapshot.ts
+++ b/src/features/snapshot.ts
@@ -47,7 +47,6 @@ export function snapshotSave(
 
   fs.mkdirSync(dir, { recursive: true });
 
-  // biome-ignore lint/suspicious/noExplicitAny: better-sqlite3 default export typing
   const db = new (Database as any)(dbPath, { readonly: true });
   try {
     db.exec(`VACUUM INTO '${dest.replace(/'/g, "''")}'`);
diff --git a/src/features/triage.ts b/src/features/triage.ts
index de3fc90e..e503261f 100644
--- a/src/features/triage.ts
+++ b/src/features/triage.ts
@@ -126,7 +126,7 @@ export function triageData(
     const minScore = opts.minScore != null ? Number(opts.minScore) : null;
     const sort = opts.sort || 'risk';
     const config = opts.config || loadConfig();
-    const riskConfig = ((config as unknown as Record<string, unknown>)['risk'] || {}) as {
+    const riskConfig = ((config as unknown as Record<string, unknown>).risk || {}) as {
       weights?: Partial<RiskWeights>;
       roleWeights?: Record<string, number>;
       defaultRoleWeight?: number;
@@ -163,7 +163,7 @@ export function triageData(
     const items = buildTriageItems(filtered, riskMetrics);
 
     const scored = minScore != null ? items.filter((it) => it.riskScore >= minScore) : items;
-    scored.sort(SORT_FNS[sort] || SORT_FNS['risk']!);
+    scored.sort(SORT_FNS[sort] || SORT_FNS.risk!);
 
     const result = {
       items: scored,
diff --git a/src/graph/algorithms/leiden/adapter.ts b/src/graph/algorithms/leiden/adapter.ts
index 5434cee0..974678f6 100644
--- a/src/graph/algorithms/leiden/adapter.ts
+++ b/src/graph/algorithms/leiden/adapter.ts
@@ -50,7 +50,7 @@ function taAdd(a: Float64Array, i: number, v: number): void {
   a[i] = taGet(a, i) + v;
 }
 
-function taSub(a: Float64Array, i: number, v: number): void {
+function _taSub(a: Float64Array, i: number, v: number): void {
   a[i] = taGet(a, i) - v;
 }
 
diff --git a/src/infrastructure/config.ts b/src/infrastructure/config.ts
index d6a7c609..181d1954 100644
--- a/src/infrastructure/config.ts
+++ b/src/infrastructure/config.ts
@@ -170,11 +170,9 @@ export function loadConfig(cwd?: string): CodegraphConfig {
         debug(`Loaded config from ${filePath}`);
         const merged = mergeConfig(DEFAULTS as unknown as Record<string, unknown>, config);
         if ('excludeTests' in config && !(config.query && 'excludeTests' in config.query)) {
-          (merged['query'] as Record<string, unknown>)['excludeTests'] = Boolean(
-            config.excludeTests,
-          );
+          (merged.query as Record<string, unknown>).excludeTests = Boolean(config.excludeTests);
         }
-        delete merged['excludeTests'];
+        delete merged.excludeTests;
         const result = resolveSecrets(applyEnvOverrides(merged as unknown as CodegraphConfig));
         _configCache.set(cwd, structuredClone(result));
         return result;
@@ -227,7 +225,7 @@ export function resolveSecrets(config: CodegraphConfig): CodegraphConfig {
       stdio: ['ignore', 'pipe', 'pipe'],
     }).trim();
     if (result) {
-      (config.llm as Record<string, unknown>)['apiKey'] = result;
+      (config.llm as Record<string, unknown>).apiKey = result;
     }
   } catch (err: unknown) {
     warn(`apiKeyCommand failed: ${(err as Error).message}`);
diff --git a/src/infrastructure/registry.ts b/src/infrastructure/registry.ts
index 365fd9c3..9b02abc8 100644
--- a/src/infrastructure/registry.ts
+++ b/src/infrastructure/registry.ts
@@ -4,7 +4,7 @@ import path from 'node:path';
 import { debug, warn } from './logger.js';
 
 export const REGISTRY_PATH: string =
-  process.env['CODEGRAPH_REGISTRY_PATH'] || path.join(os.homedir(), '.codegraph', 'registry.json');
+  process.env.CODEGRAPH_REGISTRY_PATH || path.join(os.homedir(), '.codegraph', 'registry.json');
 
 /** Default TTL: entries not accessed within 30 days are pruned. */
 export const DEFAULT_TTL_DAYS = 30;
diff --git a/src/infrastructure/update-check.ts b/src/infrastructure/update-check.ts
index 0de4c566..b0199892 100644
--- a/src/infrastructure/update-check.ts
+++ b/src/infrastructure/update-check.ts
@@ -4,7 +4,7 @@ import os from 'node:os';
 import path from 'node:path';
 
 const CACHE_PATH: string =
-  process.env['CODEGRAPH_UPDATE_CACHE_PATH'] ||
+  process.env.CODEGRAPH_UPDATE_CACHE_PATH ||
   path.join(os.homedir(), '.codegraph', 'update-check.json');
 
 const CACHE_TTL_MS = 24 * 60 * 60 * 1000; // 24 hours
@@ -120,8 +120,8 @@ export async function checkForUpdates(
   options: CheckForUpdatesOptions = {},
 ): Promise<UpdateResult | null> {
   // Suppress in non-interactive / CI contexts
-  if (process.env['CI']) return null;
-  if (process.env['NO_UPDATE_CHECK']) return null;
+  if (process.env.CI) return null;
+  if (process.env.NO_UPDATE_CHECK) return null;
   if (!process.stderr.isTTY) return null;
   if (currentVersion.includes('-')) return null;
 
diff --git a/src/mcp/server.ts b/src/mcp/server.ts
index 115c64a3..80e695ab 100644
--- a/src/mcp/server.ts
+++ b/src/mcp/server.ts
@@ -24,14 +24,11 @@ import { TOOL_HANDLERS } from './tools/index.js';
  * Because tests use vi.resetModules(), this module-level variable resets
  * on each re-import — but the process-level flag on `process` persists.
  */
-// biome-ignore lint/suspicious/noExplicitAny: MCP SDK server type is lazy-loaded
 let _activeServer: any = null;
 
 export interface McpToolContext {
   dbPath: string | undefined;
-  // biome-ignore lint/suspicious/noExplicitAny: lazy-loaded queries module
   getQueries(): Promise<any>;
-  // biome-ignore lint/suspicious/noExplicitAny: lazy-loaded better-sqlite3 constructor
   getDatabase(): any;
   findDbPath: typeof findDbPath;
   allowedRepos: string[] | undefined;
@@ -140,7 +137,6 @@ export async function startMCPServer(
   // and cached for subsequent calls.
   const { getQueries, getDatabase } = createLazyLoaders();
 
-  // biome-ignore lint/suspicious/noExplicitAny: MCP SDK types are lazy-loaded and untyped
   const server = new (Server as any)(
     { name: 'codegraph', version: PKG_VERSION },
     { capabilities: { tools: {} } },
@@ -150,7 +146,6 @@ export async function startMCPServer(
     tools: buildToolList(multiRepo),
   }));
 
-  // biome-ignore lint/suspicious/noExplicitAny: MCP SDK request type is dynamic
   server.setRequestHandler(CallToolRequestSchema, async (request: any) => {
     const { name, arguments: args } = request.params;
     try {
@@ -185,7 +180,6 @@ export async function startMCPServer(
     }
   });
 
-  // biome-ignore lint/suspicious/noExplicitAny: MCP SDK types are lazy-loaded and untyped
   const transport = new (StdioServerTransport as any)();
 
   // Graceful shutdown — when the client disconnects (e.g. session clear),
diff --git a/src/mcp/tools/audit.ts b/src/mcp/tools/audit.ts
index 1d5a54b5..6d550cac 100644
--- a/src/mcp/tools/audit.ts
+++ b/src/mcp/tools/audit.ts
@@ -19,7 +19,7 @@ export async function handler(args: AuditArgs, ctx: McpToolContext): Promise<unk
     const { explainData } = await ctx.getQueries();
     return explainData(args.target, ctx.dbPath, {
       noTests: args.no_tests,
-      limit: Math.min(args.limit ?? MCP_DEFAULTS['explain'] ?? 100, MCP_MAX_LIMIT),
+      limit: Math.min(args.limit ?? MCP_DEFAULTS.explain ?? 100, MCP_MAX_LIMIT),
       offset: effectiveOffset(args),
     });
   }
diff --git a/src/mcp/tools/cfg.ts b/src/mcp/tools/cfg.ts
index 2ac4f7df..ae94dcf8 100644
--- a/src/mcp/tools/cfg.ts
+++ b/src/mcp/tools/cfg.ts
@@ -19,7 +19,7 @@ export async function handler(args: CfgArgs, ctx: McpToolContext): Promise<unkno
     file: args.file,
     kind: args.kind,
     noTests: args.no_tests,
-    limit: Math.min(args.limit ?? MCP_DEFAULTS['query'] ?? 100, ctx.MCP_MAX_LIMIT),
+    limit: Math.min(args.limit ?? MCP_DEFAULTS.query ?? 100, ctx.MCP_MAX_LIMIT),
     offset: effectiveOffset(args),
   });
   if (args.format === 'dot') {
diff --git a/src/mcp/tools/check.ts b/src/mcp/tools/check.ts
index b477a240..cdd84b08 100644
--- a/src/mcp/tools/check.ts
+++ b/src/mcp/tools/check.ts
@@ -28,7 +28,7 @@ export async function handler(args: CheckArgs, ctx: McpToolContext): Promise<unk
       file: args.file,
       noTests: args.no_tests,
       kind: args.kind,
-      limit: Math.min(args.limit ?? MCP_DEFAULTS['manifesto'] ?? 100, MCP_MAX_LIMIT),
+      limit: Math.min(args.limit ?? MCP_DEFAULTS.manifesto ?? 100, MCP_MAX_LIMIT),
       offset: effectiveOffset(args),
     });
   }
@@ -51,7 +51,7 @@ export async function handler(args: CheckArgs, ctx: McpToolContext): Promise<unk
       file: args.file,
       noTests: args.no_tests,
       kind: args.kind,
-      limit: Math.min(args.limit ?? MCP_DEFAULTS['manifesto'] ?? 100, MCP_MAX_LIMIT),
+      limit: Math.min(args.limit ?? MCP_DEFAULTS.manifesto ?? 100, MCP_MAX_LIMIT),
       offset: effectiveOffset(args),
     });
     return { check: checkResult, manifesto: manifestoResult };
diff --git a/src/mcp/tools/dataflow.ts b/src/mcp/tools/dataflow.ts
index 3c6b0d03..b1aa313a 100644
--- a/src/mcp/tools/dataflow.ts
+++ b/src/mcp/tools/dataflow.ts
@@ -23,7 +23,7 @@ export async function handler(args: DataflowArgs, ctx: McpToolContext): Promise<
       file: args.file,
       kind: args.kind,
       noTests: args.no_tests,
-      limit: Math.min(args.limit ?? MCP_DEFAULTS['fn_impact'] ?? 100, ctx.MCP_MAX_LIMIT),
+      limit: Math.min(args.limit ?? MCP_DEFAULTS.fn_impact ?? 100, ctx.MCP_MAX_LIMIT),
       offset: effectiveOffset(args),
     });
   }
@@ -32,7 +32,7 @@ export async function handler(args: DataflowArgs, ctx: McpToolContext): Promise<
     file: args.file,
     kind: args.kind,
     noTests: args.no_tests,
-    limit: Math.min(args.limit ?? MCP_DEFAULTS['query'] ?? 100, ctx.MCP_MAX_LIMIT),
+    limit: Math.min(args.limit ?? MCP_DEFAULTS.query ?? 100, ctx.MCP_MAX_LIMIT),
     offset: effectiveOffset(args),
   });
 }
diff --git a/src/mcp/tools/export-graph.ts b/src/mcp/tools/export-graph.ts
index 958c61f1..f3ed9c73 100644
--- a/src/mcp/tools/export-graph.ts
+++ b/src/mcp/tools/export-graph.ts
@@ -19,7 +19,7 @@ export async function handler(args: ExportGraphArgs, ctx: McpToolContext): Promi
   const fileLevel = args.file_level !== false;
   const exportLimit = args.limit
     ? Math.min(args.limit, MCP_MAX_LIMIT)
-    : (MCP_DEFAULTS['export_graph'] ?? 500);
+    : (MCP_DEFAULTS.export_graph ?? 500);
 
   let result: unknown;
   try {
diff --git a/src/mcp/tools/index.ts b/src/mcp/tools/index.ts
index 0cb0c4a6..5b67bcd4 100644
--- a/src/mcp/tools/index.ts
+++ b/src/mcp/tools/index.ts
@@ -6,7 +6,6 @@ import type { McpToolContext } from '../server.js';
 
 export interface McpToolHandler {
   name: string;
-  // biome-ignore lint/suspicious/noExplicitAny: tool arg types vary per handler
   handler(args: any, ctx: McpToolContext): Promise<unknown>;
 }
 
diff --git a/src/mcp/tools/query.ts b/src/mcp/tools/query.ts
index dcf3eb30..f3d3d7e1 100644
--- a/src/mcp/tools/query.ts
+++ b/src/mcp/tools/query.ts
@@ -41,7 +41,7 @@ export async function handler(args: QueryArgs, ctx: McpToolContext): Promise<unk
     file: args.file,
     kind: args.kind,
     noTests: args.no_tests,
-    limit: Math.min(args.limit ?? MCP_DEFAULTS['query'] ?? 100, ctx.MCP_MAX_LIMIT),
+    limit: Math.min(args.limit ?? MCP_DEFAULTS.query ?? 100, ctx.MCP_MAX_LIMIT),
     offset: effectiveOffset(args),
   });
 }
diff --git a/src/mcp/tools/semantic-search.ts b/src/mcp/tools/semantic-search.ts
index 344fcc60..6c6a8afc 100644
--- a/src/mcp/tools/semantic-search.ts
+++ b/src/mcp/tools/semantic-search.ts
@@ -14,7 +14,7 @@ interface SemanticSearchArgs {
 export async function handler(args: SemanticSearchArgs, ctx: McpToolContext): Promise<unknown> {
   const mode = args.mode || 'hybrid';
   const searchOpts = {
-    limit: Math.min(args.limit ?? MCP_DEFAULTS['semantic_search'] ?? 100, ctx.MCP_MAX_LIMIT),
+    limit: Math.min(args.limit ?? MCP_DEFAULTS.semantic_search ?? 100, ctx.MCP_MAX_LIMIT),
     offset: effectiveOffset(args),
     minScore: args.min_score,
   };
diff --git a/src/mcp/tools/sequence.ts b/src/mcp/tools/sequence.ts
index e0ba93ea..5cf4f7de 100644
--- a/src/mcp/tools/sequence.ts
+++ b/src/mcp/tools/sequence.ts
@@ -23,7 +23,7 @@ export async function handler(args: SequenceArgs, ctx: McpToolContext): Promise<
     kind: args.kind,
     dataflow: args.dataflow,
     noTests: args.no_tests,
-    limit: Math.min(args.limit ?? MCP_DEFAULTS['execution_flow'] ?? 100, ctx.MCP_MAX_LIMIT),
+    limit: Math.min(args.limit ?? MCP_DEFAULTS.execution_flow ?? 100, ctx.MCP_MAX_LIMIT),
     offset: effectiveOffset(args),
   });
   return args.format === 'json' ? seqResult : { text: sequenceToMermaid(seqResult), ...seqResult };
diff --git a/src/mcp/tools/symbol-children.ts b/src/mcp/tools/symbol-children.ts
index 466081d3..fa8c8e3b 100644
--- a/src/mcp/tools/symbol-children.ts
+++ b/src/mcp/tools/symbol-children.ts
@@ -18,7 +18,7 @@ export async function handler(args: SymbolChildrenArgs, ctx: McpToolContext): Pr
     file: args.file,
     kind: args.kind,
     noTests: args.no_tests,
-    limit: Math.min(args.limit ?? MCP_DEFAULTS['context'] ?? 100, ctx.MCP_MAX_LIMIT),
+    limit: Math.min(args.limit ?? MCP_DEFAULTS.context ?? 100, ctx.MCP_MAX_LIMIT),
     offset: effectiveOffset(args),
   });
 }
diff --git a/src/mcp/tools/triage.ts b/src/mcp/tools/triage.ts
index 7e7ce3e6..e6bbd3a7 100644
--- a/src/mcp/tools/triage.ts
+++ b/src/mcp/tools/triage.ts
@@ -30,7 +30,7 @@ export async function handler(args: TriageArgs, ctx: McpToolContext): Promise<un
     return hotspotsData(ctx.dbPath, {
       metric,
       level: args.level,
-      limit: Math.min(args.limit ?? MCP_DEFAULTS['hotspots'] ?? 100, MCP_MAX_LIMIT),
+      limit: Math.min(args.limit ?? MCP_DEFAULTS.hotspots ?? 100, MCP_MAX_LIMIT),
       offset: effectiveOffset(args),
       noTests: args.no_tests,
     });
diff --git a/src/presentation/audit.ts b/src/presentation/audit.ts
index 03e6bce5..ec03818e 100644
--- a/src/presentation/audit.ts
+++ b/src/presentation/audit.ts
@@ -20,7 +20,6 @@ export function audit(
   customDbPath: string | undefined,
   opts: AuditOpts = {},
 ): void {
-  // biome-ignore lint/suspicious/noExplicitAny: audit data shape is dynamic
   const data: any = auditData(target, customDbPath, opts as any);
 
   if (outputResult(data, null, opts)) return;
diff --git a/src/presentation/diff-impact-mermaid.ts b/src/presentation/diff-impact-mermaid.ts
index 68fd9999..fade3139 100644
--- a/src/presentation/diff-impact-mermaid.ts
+++ b/src/presentation/diff-impact-mermaid.ts
@@ -10,11 +10,9 @@ export function diffImpactMermaid(
     includeImplementors?: boolean;
     limit?: number;
     offset?: number;
-    // biome-ignore lint/suspicious/noExplicitAny: config shape is dynamic
     config?: any;
   } = {},
 ): string {
-  // biome-ignore lint/suspicious/noExplicitAny: paginateResult returns dynamic shape
   const data: any = diffImpactData(customDbPath, opts);
   if ('error' in data) return data.error as string;
   if (data.changedFiles === 0 || data.affectedFunctions.length === 0) {
diff --git a/src/presentation/flow.ts b/src/presentation/flow.ts
index fcc34e66..77cd2c51 100644
--- a/src/presentation/flow.ts
+++ b/src/presentation/flow.ts
@@ -26,7 +26,6 @@ export function flow(
       noTests: opts.noTests,
       limit: opts.limit,
       offset: opts.offset,
-      // biome-ignore lint/suspicious/noExplicitAny: dynamic shape from listEntryPointsData
     }) as any;
     if (outputResult(data, 'entries', opts)) return;
     if (data.count === 0) {
@@ -56,7 +55,6 @@ export function flow(
     return;
   }
 
-  // biome-ignore lint/suspicious/noExplicitAny: dynamic shape from flowData
   const data = flowData(name, dbPath, opts) as any;
   if (outputResult(data, 'steps', opts)) return;
 
diff --git a/src/presentation/manifesto.ts b/src/presentation/manifesto.ts
index ca338e28..981c6f8a 100644
--- a/src/presentation/manifesto.ts
+++ b/src/presentation/manifesto.ts
@@ -23,7 +23,6 @@ interface ManifestoViolationRow {
 }
 
 export function manifesto(customDbPath: string | undefined, opts: ManifestoOpts = {}): void {
-  // biome-ignore lint/suspicious/noExplicitAny: dynamic shape from manifestoData
   const data = manifestoData(customDbPath, opts as any) as any;
 
   if (outputResult(data, 'violations', opts)) {
diff --git a/src/presentation/queries-cli/inspect.ts b/src/presentation/queries-cli/inspect.ts
index d95656a6..2be2905b 100644
--- a/src/presentation/queries-cli/inspect.ts
+++ b/src/presentation/queries-cli/inspect.ts
@@ -163,7 +163,6 @@ interface FunctionExplainResult extends SymbolRef {
 
 interface ExplainData {
   kind: 'file' | 'function';
-  // biome-ignore lint/suspicious/noExplicitAny: union of file/function results
   results: any[];
 }
 
diff --git a/src/presentation/result-formatter.ts b/src/presentation/result-formatter.ts
index 1f9580bc..0adf1c45 100644
--- a/src/presentation/result-formatter.ts
+++ b/src/presentation/result-formatter.ts
@@ -115,7 +115,6 @@ export interface OutputOpts {
 }
 
 export function outputResult(
-  // biome-ignore lint/suspicious/noExplicitAny: accepts any data shape from features
   data: Record<string, any>,
   field: string | null,
   opts: OutputOpts,
diff --git a/src/presentation/sequence.ts b/src/presentation/sequence.ts
index d07808a9..2010e9ea 100644
--- a/src/presentation/sequence.ts
+++ b/src/presentation/sequence.ts
@@ -16,7 +16,6 @@ interface SequenceOpts {
 }
 
 export function sequence(name: string, dbPath: string | undefined, opts: SequenceOpts = {}): void {
-  // biome-ignore lint/suspicious/noExplicitAny: dynamic shape from sequenceData
   const data = sequenceData(name, dbPath, opts) as any;
 
   if (outputResult(data, 'messages', opts)) return;
diff --git a/src/presentation/structure.ts b/src/presentation/structure.ts
index 806bbfb0..b5208d48 100644
--- a/src/presentation/structure.ts
+++ b/src/presentation/structure.ts
@@ -49,22 +49,10 @@ export function formatStructure(data: StructureResult): string {
   return lines.join('\n');
 }
 
-interface HotspotEntry {
-  name: string;
-  kind: string;
-  fileCount?: number;
-  cohesion?: number | null;
-  lineCount?: number;
-  symbolCount?: number;
-  fanIn?: number;
-  fanOut?: number;
-}
-
 interface HotspotsResult {
   metric: string;
   level: string;
   limit: number;
-  // biome-ignore lint/suspicious/noExplicitAny: hotspots shape varies by level
   hotspots: any[];
 }
 
diff --git a/src/presentation/triage.ts b/src/presentation/triage.ts
index ca21a4b2..11353c09 100644
--- a/src/presentation/triage.ts
+++ b/src/presentation/triage.ts
@@ -37,7 +37,6 @@ interface TriageSummary {
 }
 
 export function triage(customDbPath: string | undefined, opts: TriageOpts = {}): void {
-  // biome-ignore lint/suspicious/noExplicitAny: dynamic shape from triageData
   const data = triageData(customDbPath, opts as any) as {
     items: TriageItem[];
     summary: TriageSummary;
diff --git a/src/types.ts b/src/types.ts
index 3b91bf9d..f4cacb5d 100644
--- a/src/types.ts
+++ b/src/types.ts
@@ -1774,7 +1774,6 @@ export interface BetterSqlite3Database {
   exec(sql: string): this;
   close(): void;
   pragma(sql: string): unknown;
-  // biome-ignore lint/suspicious/noExplicitAny: must be compatible with better-sqlite3's generic Transaction<F> return type
   transaction<F extends (...args: any[]) => any>(fn: F): F;
   readonly open: boolean;
   readonly name: string;
@@ -1819,14 +1818,10 @@ export interface NativeParseTreeCache {
 
 /** Shared context passed to every CLI command's execute/validate functions. */
 export interface CommandContext {
-  // biome-ignore lint/suspicious/noExplicitAny: config is a deeply nested dynamic object
   config: Record<string, any>;
-  // biome-ignore lint/suspicious/noExplicitAny: Commander options are dynamically typed
   resolveNoTests: (opts: any) => boolean;
-  // biome-ignore lint/suspicious/noExplicitAny: Commander options are dynamically typed
   resolveQueryOpts: (opts: any) => any;
   formatSize: (bytes: number) => string;
-  // biome-ignore lint/suspicious/noExplicitAny: data shapes vary per command
   outputResult: (data: any, key: string, opts: any) => boolean;
   program: import('commander').Command;
 }
@@ -1839,12 +1834,9 @@ export interface CommandDefinition {
   options?: Array<
     | [string, string]
     | [string, string, string | boolean | number]
-    // biome-ignore lint/suspicious/noExplicitAny: Commander parse functions accept arbitrary return types
     | [string, string, (val: string) => any, string | boolean | number]
   >;
-  // biome-ignore lint/suspicious/noExplicitAny: Commander options are dynamically typed
-  validate?: (args: any[], opts: any, ctx: CommandContext) => string | undefined | void;
-  // biome-ignore lint/suspicious/noExplicitAny: Commander options are dynamically typed
+  validate?: (args: any[], opts: any, ctx: CommandContext) => string | undefined | undefined;
   execute?: (args: any[], opts: any, ctx: CommandContext) => void | Promise<void>;
   subcommands?: CommandDefinition[];
 }
diff --git a/src/vendor.d.ts b/src/vendor.d.ts
index 28c247f6..2a8e8599 100644
--- a/src/vendor.d.ts
+++ b/src/vendor.d.ts
@@ -9,7 +9,6 @@ declare module 'better-sqlite3' {
     interface Database {
       prepare<TRow = unknown>(sql: string): Statement<TRow>;
       exec(sql: string): Database;
-      // biome-ignore lint/suspicious/noExplicitAny: must match better-sqlite3's generic Transaction<F>
       transaction<F extends (...args: any[]) => any>(fn: F): F;
       close(): void;
       pragma(pragma: string, options?: { simple?: boolean }): unknown;

From 6e3d0a902d0ff2b99adf2b3d698dc342dc1c644e Mon Sep 17 00:00:00 2001
From: carlos-alm <127798846+carlos-alm@users.noreply.github.com>
Date: Thu, 26 Mar 2026 03:05:29 -0600
Subject: [PATCH 3/4] fix: disable noPropertyAccessFromIndexSignature, clean up
 useLiteralKeys suppressions (#629)

tsconfig's noPropertyAccessFromIndexSignature conflicted with biome's
useLiteralKeys auto-fix, causing TS4111 errors on CI. Disable the TS
rule so dot notation is valid for index signatures. Remove all
now-unnecessary useLiteralKeys biome-ignore comments and convert
remaining bracket notation. Also fix duplicate | undefined in types.ts
and delete dead _taSub function in leiden adapter.
---
 src/ast-analysis/engine.ts             |  9 +++------
 src/features/cfg.ts                    |  6 ++----
 src/features/complexity.ts             |  3 +--
 src/graph/algorithms/leiden/adapter.ts | 11 ++---------
 src/mcp/server.ts                      |  6 ++----
 src/types.ts                           |  2 +-
 tsconfig.json                          |  2 +-
 7 files changed, 12 insertions(+), 27 deletions(-)

diff --git a/src/ast-analysis/engine.ts b/src/ast-analysis/engine.ts
index fe0b609e..fdee6cae 100644
--- a/src/ast-analysis/engine.ts
+++ b/src/ast-analysis/engine.ts
@@ -259,8 +259,7 @@ function setupVisitors(
 // ─── Result storage helpers ─────────────────────────────────────────────
 
 function storeComplexityResults(results: WalkResults, defs: Definition[], langId: string): void {
-  // biome-ignore lint/complexity/useLiteralKeys: bracket notation required by noPropertyAccessFromIndexSignature
-  const complexityResults = (results['complexity'] || []) as ComplexityFuncResult[];
+  const complexityResults = (results.complexity || []) as ComplexityFuncResult[];
   const resultByLine = new Map<number, ComplexityFuncResult[]>();
   for (const r of complexityResults) {
     if (r.funcNode) {
@@ -301,8 +300,7 @@ function storeComplexityResults(results: WalkResults, defs: Definition[], langId
 }
 
 function storeCfgResults(results: WalkResults, defs: Definition[]): void {
-  // biome-ignore lint/complexity/useLiteralKeys: bracket notation required by noPropertyAccessFromIndexSignature
-  const cfgResults = (results['cfg'] || []) as CfgFuncResult[];
+  const cfgResults = (results.cfg || []) as CfgFuncResult[];
   const cfgByLine = new Map<number, CfgFuncResult[]>();
   for (const r of cfgResults) {
     if (r.funcNode) {
@@ -450,8 +448,7 @@ export async function runAnalyses(
 
     if (complexityVisitor) storeComplexityResults(results, defs, langId);
     if (cfgVisitor) storeCfgResults(results, defs);
-    // biome-ignore lint/complexity/useLiteralKeys: bracket notation required by noPropertyAccessFromIndexSignature
-    if (dataflowVisitor) symbols.dataflow = results['dataflow'] as DataflowResult;
+    if (dataflowVisitor) symbols.dataflow = results.dataflow as DataflowResult;
   }
 
   timing._unifiedWalkMs = performance.now() - t0walk;
diff --git a/src/features/cfg.ts b/src/features/cfg.ts
index 278679ab..389ee3c2 100644
--- a/src/features/cfg.ts
+++ b/src/features/cfg.ts
@@ -62,8 +62,7 @@ export function buildFunctionCFG(functionNode: TreeSitterNode, langId: string):
   };
 
   const results = walkWithVisitors(functionNode, [visitor], langId, walkerOpts);
-  // biome-ignore lint/complexity/useLiteralKeys: noPropertyAccessFromIndexSignature requires bracket notation
-  const cfgResults = (results['cfg'] || []) as Array<{
+  const cfgResults = (results.cfg || []) as Array<{
     funcNode: TreeSitterNode;
     blocks: CfgBuildBlock[];
     edges: CfgBuildEdge[];
@@ -214,8 +213,7 @@ function buildVisitorCfgMap(
     },
   };
   const walkResults = walkWithVisitors(tree?.rootNode, [visitor], langId, walkerOpts);
-  // biome-ignore lint/complexity/useLiteralKeys: noPropertyAccessFromIndexSignature requires bracket notation
-  const cfgResults = (walkResults['cfg'] || []) as VisitorCfgResult[];
+  const cfgResults = (walkResults.cfg || []) as VisitorCfgResult[];
   const visitorCfgByLine = new Map<number, VisitorCfgResult[]>();
   for (const r of cfgResults) {
     if (r.funcNode) {
diff --git a/src/features/complexity.ts b/src/features/complexity.ts
index bd4a27b0..b0a1d05e 100644
--- a/src/features/complexity.ts
+++ b/src/features/complexity.ts
@@ -300,8 +300,7 @@ export function computeAllMetrics(
     nestingNodeTypes: nestingNodes,
   });
 
-  // biome-ignore lint/complexity/useLiteralKeys: noPropertyAccessFromIndexSignature requires bracket notation
-  const rawResult = results['complexity'] as {
+  const rawResult = results.complexity as {
     cognitive: number;
     cyclomatic: number;
     maxNesting: number;
diff --git a/src/graph/algorithms/leiden/adapter.ts b/src/graph/algorithms/leiden/adapter.ts
index 974678f6..1661cab2 100644
--- a/src/graph/algorithms/leiden/adapter.ts
+++ b/src/graph/algorithms/leiden/adapter.ts
@@ -50,18 +50,11 @@ function taAdd(a: Float64Array, i: number, v: number): void {
   a[i] = taGet(a, i) + v;
 }
 
-function _taSub(a: Float64Array, i: number, v: number): void {
-  a[i] = taGet(a, i) - v;
-}
-
 export function makeGraphAdapter(graph: CodeGraph, opts: GraphAdapterOptions = {}): GraphAdapter {
   const linkWeight: (attrs: EdgeAttrs) => number =
-    opts.linkWeight ||
-    // biome-ignore lint/complexity/useLiteralKeys: index signature requires bracket access
-    ((attrs) => (attrs && typeof attrs['weight'] === 'number' ? attrs['weight'] : 1));
+    opts.linkWeight || ((attrs) => (attrs && typeof attrs.weight === 'number' ? attrs.weight : 1));
   const nodeSize: (attrs: NodeAttrs) => number =
-    // biome-ignore lint/complexity/useLiteralKeys: index signature requires bracket access
-    opts.nodeSize || ((attrs) => (attrs && typeof attrs['size'] === 'number' ? attrs['size'] : 1));
+    opts.nodeSize || ((attrs) => (attrs && typeof attrs.size === 'number' ? attrs.size : 1));
   const directed: boolean = !!opts.directed;
   const baseNodeIds: string[] | undefined = opts.baseNodeIds;
 
diff --git a/src/mcp/server.ts b/src/mcp/server.ts
index 80e695ab..b890eb9f 100644
--- a/src/mcp/server.ts
+++ b/src/mcp/server.ts
@@ -191,10 +191,8 @@ export async function startMCPServer(
   // Register handlers once per process to avoid listener accumulation.
   // Use a process-level flag so it survives vi.resetModules() in tests.
   const g = globalThis as Record<string, unknown>;
-  // biome-ignore lint/complexity/useLiteralKeys: bracket notation required by TS noPropertyAccessFromIndexSignature
-  if (!g['__codegraph_shutdown_installed']) {
-    // biome-ignore lint/complexity/useLiteralKeys: bracket notation required by TS noPropertyAccessFromIndexSignature
-    g['__codegraph_shutdown_installed'] = true;
+  if (!g.__codegraph_shutdown_installed) {
+    g.__codegraph_shutdown_installed = true;
 
     const shutdown = async () => {
       try {
diff --git a/src/types.ts b/src/types.ts
index f4cacb5d..0acc131d 100644
--- a/src/types.ts
+++ b/src/types.ts
@@ -1836,7 +1836,7 @@ export interface CommandDefinition {
     | [string, string, string | boolean | number]
     | [string, string, (val: string) => any, string | boolean | number]
   >;
-  validate?: (args: any[], opts: any, ctx: CommandContext) => string | undefined | undefined;
+  validate?: (args: any[], opts: any, ctx: CommandContext) => string | undefined;
   execute?: (args: any[], opts: any, ctx: CommandContext) => void | Promise<void>;
   subcommands?: CommandDefinition[];
 }
diff --git a/tsconfig.json b/tsconfig.json
index 99220394..8967f82c 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -41,7 +41,7 @@
     /* Type Checking — strict mode */
     "strict": true,
     "noUncheckedIndexedAccess": true,
-    "noPropertyAccessFromIndexSignature": true,
+    "noPropertyAccessFromIndexSignature": false,
     "exactOptionalPropertyTypes": false,
 
     /* Misc */

From 0b8425c2d519da2a6a88ea843a86d18cd3ab4a6b Mon Sep 17 00:00:00 2001
From: carlos-alm <127798846+carlos-alm@users.noreply.github.com>
Date: Thu, 26 Mar 2026 03:09:44 -0600
Subject: [PATCH 4/4] fix: make WASM build non-fatal without bash-only syntax
 (#629)

The prepare script used bash-style (cmd || echo) which fails on Windows
cmd.exe. Instead, make build-wasm.ts always exit 0 since failures are
already non-fatal by design (per-grammar try/catch with warning logs).
This restores the simple prepare script while keeping WASM resilience.
---
 package.json          | 2 +-
 scripts/build-wasm.ts | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/package.json b/package.json
index a2d6bf9c..af3a1442 100644
--- a/package.json
+++ b/package.json
@@ -41,7 +41,7 @@
     "format": "biome format --write src/ tests/",
     "prepack": "npm run build",
     "clean": "node -e \"require('fs').rmSync('dist',{recursive:true,force:true});require('fs').rmSync('.tsbuildinfo',{force:true})\"",
-    "prepare": "(npm run build:wasm || echo 'WARN: WASM grammar build failed (non-fatal — native engine available)') && npm run build && husky && npm run deps:tree",
+    "prepare": "npm run build:wasm && npm run build && husky && npm run deps:tree",
     "deps:tree": "node scripts/node-ts.js scripts/gen-deps.ts",
     "benchmark": "node --experimental-strip-types --import ./scripts/ts-resolve-loader.js scripts/benchmark.ts",
     "release": "commit-and-tag-version",
diff --git a/scripts/build-wasm.ts b/scripts/build-wasm.ts
index cc0268e9..c2fbd997 100644
--- a/scripts/build-wasm.ts
+++ b/scripts/build-wasm.ts
@@ -57,7 +57,6 @@ for (const g of grammars) {
 
 if (failed > 0) {
   console.warn(`\n${failed}/${grammars.length} grammars failed to build (non-fatal — native engine available)`);
-  process.exitCode = 1;
 } else {
   console.log('\nAll grammars built successfully into grammars/');
 }