diff --git a/packages/cli/src/commands/explain.ts b/packages/cli/src/commands/explain.ts
index cf43d20a..10ac1cc3 100644
--- a/packages/cli/src/commands/explain.ts
+++ b/packages/cli/src/commands/explain.ts
@@ -6,7 +6,7 @@ import { findDuplicateKeys } from '../core/duplicates.js';
 import type { ScanOptions } from '../config/types.js';
 import { DEFAULT_ENV_FILE, DEFAULT_EXAMPLE_FILE } from '../config/constants.js';
 import { printExplain, type ExplainResult } from '../ui/scan/printExplain.js';
-import { skipCommentedUsages } from '../core/helpers/skipCommentedUsages.js';
+import { skipCommentedUsages } from '../core/scan/skipCommentedUsages.js';
 
 /**
  * Options forwarded from the CLI for the --explain command.
diff --git a/packages/cli/src/commands/scanUsage.ts b/packages/cli/src/commands/scanUsage.ts
index 39661346..76d50daf 100644
--- a/packages/cli/src/commands/scanUsage.ts
+++ b/packages/cli/src/commands/scanUsage.ts
@@ -12,7 +12,7 @@ import { scanJsonOutput } from '../ui/scan/scanJsonOutput.js';
 import { printMissingExample } from '../ui/scan/printMissingExample.js';
 import { processComparisonFile } from '../services/processComparisonFile.js';
 import { printComparisonError } from '../ui/scan/printComparisonError.js';
-import { skipCommentedUsages } from '../core/helpers/skipCommentedUsages.js';
+import { skipCommentedUsages } from '../core/scan/skipCommentedUsages.js';
 import { frameworkValidator } from '../core/frameworks/frameworkValidator.js';
 import { detectSecretsInExample } from '../core/security/exampleSecretDetector.js';
 import {
diff --git a/packages/cli/src/core/compare/parseAndFilterEnv.ts b/packages/cli/src/core/compare/parseAndFilterEnv.ts
index b40c635f..d0de996e 100644
--- a/packages/cli/src/core/compare/parseAndFilterEnv.ts
+++ b/packages/cli/src/core/compare/parseAndFilterEnv.ts
@@ -1,5 +1,5 @@
 import { parseEnvFile } from '../../services/parseEnvFile.js';
-import { filterIgnoredKeys } from '../filterIgnoredKeys.js';
+import { filterIgnoredKeys } from '../helpers/filterIgnoredKeys.js';
 import type { ComparisonOptions } from '../../config/types.js';
 
 /**
diff --git a/packages/cli/src/core/filterIgnoredKeys.ts b/packages/cli/src/core/helpers/filterIgnoredKeys.ts
similarity index 100%
rename from packages/cli/src/core/filterIgnoredKeys.ts
rename to packages/cli/src/core/helpers/filterIgnoredKeys.ts
diff --git a/packages/cli/src/core/scan/compareScan.ts b/packages/cli/src/core/scan/compareScan.ts
index 8cf9cad7..c1438050 100644
--- a/packages/cli/src/core/scan/compareScan.ts
+++ b/packages/cli/src/core/scan/compareScan.ts
@@ -1,5 +1,5 @@
 import type { ScanResult } from '../../config/types.js';
-import { filterIgnoredKeys } from '../filterIgnoredKeys.js';
+import { filterIgnoredKeys } from '../helpers/filterIgnoredKeys.js';
 
 /**
  * Compares the scan result with the environment variables.
diff --git a/packages/cli/src/core/helpers/skipCommentedUsages.ts b/packages/cli/src/core/scan/skipCommentedUsages.ts
similarity index 100%
rename from packages/cli/src/core/helpers/skipCommentedUsages.ts
rename to packages/cli/src/core/scan/skipCommentedUsages.ts
diff --git a/packages/cli/src/services/processComparisonFile.ts b/packages/cli/src/services/processComparisonFile.ts
index 1c4d4038..c5b5dcd7 100644
--- a/packages/cli/src/services/processComparisonFile.ts
+++ b/packages/cli/src/services/processComparisonFile.ts
@@ -1,6 +1,6 @@
 import fs from 'fs';
 import { parseEnvFile } from './parseEnvFile.js';
-import { filterIgnoredKeys } from '../core/filterIgnoredKeys.js';
+import { filterIgnoredKeys } from '../core/helpers/filterIgnoredKeys.js';
 import { compareWithEnvFiles } from '../core/scan/compareScan.js';
 import { findDuplicateKeys } from '../core/duplicates.js';
 import { applyFixes } from '../core/fixEnv.js';
diff --git a/packages/cli/src/services/scanCodebase.ts b/packages/cli/src/services/scanCodebase.ts
index 97e1e2b0..24b617cf 100644
--- a/packages/cli/src/services/scanCodebase.ts
+++ b/packages/cli/src/services/scanCodebase.ts
@@ -1,7 +1,7 @@
 import fs from 'fs/promises';
 import path from 'path';
 import type { EnvUsage, ScanOptions, ScanResult } from '../config/types.js';
-import { DEFAULT_EXCLUDE_KEYS } from '../core/filterIgnoredKeys.js';
+import { DEFAULT_EXCLUDE_KEYS } from '../core/helpers/filterIgnoredKeys.js';
 import {
   detectSecretsInSource,
   type SecretFinding,
diff --git a/packages/cli/test/unit/commands/compare.test.ts b/packages/cli/test/unit/commands/compare.test.ts
index 6efde99e..92fbaec4 100644
--- a/packages/cli/test/unit/commands/compare.test.ts
+++ b/packages/cli/test/unit/commands/compare.test.ts
@@ -26,7 +26,7 @@ vi.mock('../../../src/core/duplicates.js', () => ({
   findDuplicateKeys: vi.fn(),
 }));
 
-vi.mock('../../../src/core/filterIgnoredKeys.js', () => ({
+vi.mock('../../../src/core/helpers/filterIgnoredKeys.js', () => ({
   filterIgnoredKeys: vi.fn((keys) => keys),
 }));
 
@@ -82,7 +82,7 @@ import { parseEnvFile } from '../../../src/services/parseEnvFile.js';
 import { diffEnv } from '../../../src/core/diffEnv.js';
 import { checkGitignoreStatus } from '../../../src/services/git.js';
 import { findDuplicateKeys } from '../../../src/core/duplicates.js';
-import { filterIgnoredKeys } from '../../../src/core/filterIgnoredKeys.js';
+import { filterIgnoredKeys } from '../../../src/core/helpers/filterIgnoredKeys.js';
 import { updateTotals } from '../../../src/core/compare/updateTotals.js';
 import { applyFixes } from '../../../src/core/fixEnv.js';
 import { printFixTips } from '../../../src/ui/shared/printFixTips.js';
diff --git a/packages/cli/test/unit/commands/explain.test.ts b/packages/cli/test/unit/commands/explain.test.ts
index 94bc46d6..934a2589 100644
--- a/packages/cli/test/unit/commands/explain.test.ts
+++ b/packages/cli/test/unit/commands/explain.test.ts
@@ -16,7 +16,7 @@ vi.mock('../../../src/core/duplicates.js', () => ({
   findDuplicateKeys: vi.fn(),
 }));
 
-vi.mock('../../../src/core/helpers/skipCommentedUsages.js', () => ({
+vi.mock('../../../src/core/scan/skipCommentedUsages.js', () => ({
   skipCommentedUsages: vi.fn((usages) => usages),
 }));
 
@@ -27,7 +27,7 @@ vi.mock('../../../src/ui/scan/printExplain.js', () => ({
 import { scanCodebase } from '../../../src/services/scanCodebase.js';
 import { parseEnvFile } from '../../../src/services/parseEnvFile.js';
 import { findDuplicateKeys } from '../../../src/core/duplicates.js';
-import { skipCommentedUsages } from '../../../src/core/helpers/skipCommentedUsages.js';
+import { skipCommentedUsages } from '../../../src/core/scan/skipCommentedUsages.js';
 import { printExplain } from '../../../src/ui/scan/printExplain.js';
 
 const mockScanCodebase = scanCodebase as ReturnType<typeof vi.fn>;
diff --git a/packages/cli/test/unit/core/filterIgnoredKeys.test.ts b/packages/cli/test/unit/core/filterIgnoredKeys.test.ts
index ea344b8b..70ad1dc1 100644
--- a/packages/cli/test/unit/core/filterIgnoredKeys.test.ts
+++ b/packages/cli/test/unit/core/filterIgnoredKeys.test.ts
@@ -1,5 +1,5 @@
 import { describe, it, expect } from 'vitest';
-import { filterIgnoredKeys } from '../../../src/core/filterIgnoredKeys.js';
+import { filterIgnoredKeys } from '../../../src/core/helpers/filterIgnoredKeys.js';
 
 describe('filterIgnoredKeys', () => {
   it('filters exact and regex matches', () => {