diff --git a/eslint.config.mjs b/eslint.config.mjs
index 58306da60..8d1046583 100644
--- a/eslint.config.mjs
+++ b/eslint.config.mjs
@@ -67,22 +67,15 @@ export default [
     },
   },
 
-  // Forcing function for the pino migration: warn on any new `console.*` in
-  // core source. Existing call sites carry an eslint-disable-next-line comment
-  // tagged `TODO(pino-migration)` so a `git grep` inventories what's left.
-  // Tests, bin scripts, and the logger module itself are exempt.
-  // CLI/server are exempt above (legitimate stdout output).
-  // Severity is `warn` (not `error`) for the baseline; future PRs can flip to
-  // `error` once the migration sweep lands.
+  // Forcing function for the pino migration. Severity is `error` — the
+  // codebase-wide migration is complete; new `console.*` in core source
+  // must fail lint. CLI/server are exempt above (legitimate stdout output).
+  // Tests, bin scripts, and the logger module itself remain exempt.
   {
     files: ['gitnexus/src/**/*.ts'],
-    ignores: [
-      'gitnexus/src/cli/**',
-      'gitnexus/src/server/**',
-      'gitnexus/src/core/logger.ts',
-    ],
+    ignores: ['gitnexus/src/cli/**', 'gitnexus/src/server/**', 'gitnexus/src/core/logger.ts'],
     rules: {
-      'no-console': 'warn',
+      'no-console': 'error',
     },
   },
 
diff --git a/gitnexus/src/config/ignore-service.ts b/gitnexus/src/config/ignore-service.ts
index f44a66cbd..ce1fda913 100644
--- a/gitnexus/src/config/ignore-service.ts
+++ b/gitnexus/src/config/ignore-service.ts
@@ -2,6 +2,7 @@ import ignore, { type Ignore } from 'ignore';
 import fs from 'fs/promises';
 import nodePath from 'path';
 import type { Path } from 'path-scurry';
+import { logger } from '../core/logger.js';
 
 const DEFAULT_IGNORE_LIST = new Set([
   // Version Control
@@ -365,8 +366,7 @@ export const loadIgnoreRules = async (
     } catch (err: unknown) {
       const code = (err as NodeJS.ErrnoException).code;
       if (code !== 'ENOENT') {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.warn(`  Warning: could not read ${filename}: ${(err as Error).message}`);
+        logger.warn(`  Warning: could not read ${filename}: ${(err as Error).message}`);
       }
     }
   }
diff --git a/gitnexus/src/core/embeddings/embedder.ts b/gitnexus/src/core/embeddings/embedder.ts
index a4fe1cf1d..b37fb45f3 100644
--- a/gitnexus/src/core/embeddings/embedder.ts
+++ b/gitnexus/src/core/embeddings/embedder.ts
@@ -23,6 +23,7 @@ import { DEFAULT_EMBEDDING_CONFIG, type EmbeddingConfig, type ModelProgress } fr
 import { isHttpMode, getHttpDimensions, httpEmbed } from './http-client.js';
 import { resolveEmbeddingConfig } from './config.js';
 import { applyHfEnvOverrides } from './hf-env.js';
+import { logger } from '../logger.js';
 
 /**
  * Check whether the onnxruntime-node package that @huggingface/transformers
@@ -166,8 +167,7 @@ export const initEmbedder = async (
 
       const isDev = process.env.NODE_ENV === 'development';
       if (isDev) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.log(`🧠 Loading embedding model: ${finalConfig.modelId}`);
+        logger.info(`🧠 Loading embedding model: ${finalConfig.modelId}`);
       }
 
       const progressCallback = onProgress
@@ -193,17 +193,13 @@ export const initEmbedder = async (
       for (const device of devicesToTry) {
         try {
           if (isDev && device === 'dml') {
-            // eslint-disable-next-line no-console -- TODO(pino-migration)
-            console.log('🔧 Trying DirectML (DirectX12) GPU backend...');
+            logger.info('🔧 Trying DirectML (DirectX12) GPU backend...');
           } else if (isDev && device === 'cuda') {
-            // eslint-disable-next-line no-console -- TODO(pino-migration)
-            console.log('🔧 Trying CUDA GPU backend...');
+            logger.info('🔧 Trying CUDA GPU backend...');
           } else if (isDev && device === 'cpu') {
-            // eslint-disable-next-line no-console -- TODO(pino-migration)
-            console.log('🔧 Using CPU backend...');
+            logger.info('🔧 Using CPU backend...');
           } else if (isDev && device === 'wasm') {
-            // eslint-disable-next-line no-console -- TODO(pino-migration)
-            console.log('🔧 Using WASM backend (slower)...');
+            logger.info('🔧 Using WASM backend (slower)...');
           }
 
           embedderInstance = await (pipeline as any)('feature-extraction', finalConfig.modelId, {
@@ -226,18 +222,15 @@ export const initEmbedder = async (
                 : device === 'cuda'
                   ? 'GPU (CUDA)'
                   : device.toUpperCase();
-            // eslint-disable-next-line no-console -- TODO(pino-migration)
-            console.log(`✅ Using ${label} backend`);
-            // eslint-disable-next-line no-console -- TODO(pino-migration)
-            console.log('✅ Embedding model loaded successfully');
+            logger.info(`✅ Using ${label} backend`);
+            logger.info('✅ Embedding model loaded successfully');
           }
 
           return embedderInstance!;
         } catch (deviceError) {
           if (isDev && (device === 'cuda' || device === 'dml')) {
             const gpuType = device === 'dml' ? 'DirectML' : 'CUDA';
-            // eslint-disable-next-line no-console -- TODO(pino-migration)
-            console.log(`⚠️  ${gpuType} not available, falling back to CPU...`);
+            logger.info(`⚠️  ${gpuType} not available, falling back to CPU...`);
           }
           // Continue to next device in list
           if (device === devicesToTry[devicesToTry.length - 1]) {
diff --git a/gitnexus/src/core/embeddings/embedding-pipeline.ts b/gitnexus/src/core/embeddings/embedding-pipeline.ts
index f83239650..bcb072c50 100644
--- a/gitnexus/src/core/embeddings/embedding-pipeline.ts
+++ b/gitnexus/src/core/embeddings/embedding-pipeline.ts
@@ -44,6 +44,7 @@ import {
 } from '../lbug/schema.js';
 import { loadVectorExtension } from '../lbug/lbug-adapter.js';
 import { getExactScanLimit } from '../platform/capabilities.js';
+import { logger } from '../logger.js';
 
 const isDev = process.env.NODE_ENV === 'development';
 
@@ -157,8 +158,7 @@ const queryEmbeddableNodes = async (
       }
     } catch (error) {
       if (isDev) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.warn(`Query for ${label} nodes failed:`, error);
+        logger.warn({ error }, `Query for ${label} nodes failed:`);
       }
     }
   }
@@ -213,8 +213,7 @@ const createVectorIndex = async (
     return true;
   } catch (error) {
     if (isDev) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn('Vector index creation warning:', error);
+      logger.warn({ error }, 'Vector index creation warning:');
     }
     return false;
   }
@@ -258,8 +257,7 @@ export const runEmbeddingPipeline = async (
 
   try {
     const vectorAvailable = await ensureVectorExtensionAvailable();
-    // eslint-disable-next-line no-console -- TODO(pino-migration)
-    if (!vectorAvailable && isDev) console.warn(vectorUnavailableMessage);
+    logger.warn(vectorUnavailableMessage);
 
     // Phase 1: Load embedding model
     onProgress({
@@ -286,8 +284,7 @@ export const runEmbeddingPipeline = async (
     });
 
     if (isDev) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.log('🔍 Querying embeddable nodes...');
+      logger.info('🔍 Querying embeddable nodes...');
     }
 
     // Phase 2: Query embeddable nodes
@@ -329,8 +326,7 @@ export const runEmbeddingPipeline = async (
       // (Kuzu forbids SET on vector-indexed properties; DELETE-then-INSERT is the sanctioned pattern)
       if (staleNodeIds.length > 0) {
         if (isDev) {
-          // eslint-disable-next-line no-console -- TODO(pino-migration)
-          console.log(`🔄 Deleting ${staleNodeIds.length} stale embedding rows for re-embed`);
+          logger.info(`🔄 Deleting ${staleNodeIds.length} stale embedding rows for re-embed`);
         }
         try {
           await executeWithReusedStatement(
@@ -351,8 +347,7 @@ export const runEmbeddingPipeline = async (
       }
 
       if (isDev) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.log(
+        logger.info(
           `📦 Incremental embeddings: ${beforeCount} total, ${existingEmbeddings.size} cached, ${staleNodeIds.length} stale, ${nodes.length} to embed`,
         );
       }
@@ -361,8 +356,7 @@ export const runEmbeddingPipeline = async (
     const totalNodes = nodes.length;
 
     if (isDev) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.log(`📊 Found ${totalNodes} embeddable nodes`);
+      logger.info(`📊 Found ${totalNodes} embeddable nodes`);
     }
 
     if (totalNodes === 0) {
@@ -449,10 +443,9 @@ export const runEmbeddingPipeline = async (
             );
           } catch (chunkErr) {
             if (isDev) {
-              // eslint-disable-next-line no-console -- TODO(pino-migration)
-              console.warn(
+              logger.warn(
+                { chunkErr },
                 `⚠️ AST chunking failed for ${node.label} "${node.name}" (${node.filePath}), falling back to character-based chunking:`,
-                chunkErr,
               );
             }
             chunks = characterChunk(node.content, startLine, endLine, chunkSize, overlap);
@@ -490,10 +483,9 @@ export const runEmbeddingPipeline = async (
         try {
           embeddings = await embedBatch(subTexts);
         } catch (embedErr) {
-          // eslint-disable-next-line no-console -- TODO(pino-migration)
-          console.error(
+          logger.error(
+            { embedErr },
             `❌ embedBatch failed for ${subTexts.length} texts (first: "${subTexts[0]?.substring(0, 80)}..."):`,
-            embedErr,
           );
           throw embedErr;
         }
@@ -529,8 +521,7 @@ export const runEmbeddingPipeline = async (
     });
 
     if (isDev) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.log('📇 Creating vector index...');
+      logger.info('📇 Creating vector index...');
     }
 
     const vectorIndexReady = await createVectorIndex(executeQuery);
@@ -543,8 +534,7 @@ export const runEmbeddingPipeline = async (
     });
 
     if (isDev) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.log(
+      logger.info(
         `✅ Embedding pipeline complete! (${totalChunks} chunks from ${totalNodes} nodes)`,
       );
     }
@@ -558,8 +548,7 @@ export const runEmbeddingPipeline = async (
     const errorMessage = error instanceof Error ? error.message : 'Unknown error';
 
     if (isDev) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.error('❌ Embedding pipeline error:', error);
+      logger.error({ error }, '❌ Embedding pipeline error:');
     }
 
     onProgress({
diff --git a/gitnexus/src/core/group/extractors/elixir-workspace-extractor.ts b/gitnexus/src/core/group/extractors/elixir-workspace-extractor.ts
index d509a5870..7c184ba96 100644
--- a/gitnexus/src/core/group/extractors/elixir-workspace-extractor.ts
+++ b/gitnexus/src/core/group/extractors/elixir-workspace-extractor.ts
@@ -4,6 +4,7 @@ import type { CypherExecutor } from '../contract-extractor.js';
 import type { GroupManifestLink, ContractRole } from '../types.js';
 import { shouldIgnorePath, loadIgnoreRules } from '../../../config/ignore-service.js';
 
+import { logger } from '../../logger.js';
 interface ElixirAppMeta {
   appName: string;
   modulePrefix: string;
@@ -202,8 +203,7 @@ export async function extractElixirWorkspaceLinks(
     };
     const existing = appsByName.get(manifest.appName);
     if (existing) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(
+      logger.warn(
         `[elixir-workspace-extractor] duplicate app "${manifest.appName}" in "${groupPath}" and "${existing.groupPath}" — skipping "${groupPath}"`,
       );
       continue;
diff --git a/gitnexus/src/core/group/extractors/go-workspace-extractor.ts b/gitnexus/src/core/group/extractors/go-workspace-extractor.ts
index adc339850..55e870090 100644
--- a/gitnexus/src/core/group/extractors/go-workspace-extractor.ts
+++ b/gitnexus/src/core/group/extractors/go-workspace-extractor.ts
@@ -4,6 +4,7 @@ import type { CypherExecutor } from '../contract-extractor.js';
 import type { GroupManifestLink, ContractRole } from '../types.js';
 import { shouldIgnorePath, loadIgnoreRules } from '../../../config/ignore-service.js';
 
+import { logger } from '../../logger.js';
 interface GoModuleMeta {
   modulePath: string;
   groupPath: string;
@@ -211,8 +212,7 @@ export async function extractGoWorkspaceLinks(
     };
     const existing = modulesByPath.get(manifest.modulePath);
     if (existing) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(
+      logger.warn(
         `[go-workspace-extractor] duplicate module "${manifest.modulePath}" in "${groupPath}" and "${existing.groupPath}" — skipping "${groupPath}"`,
       );
       continue;
diff --git a/gitnexus/src/core/group/extractors/grpc-extractor.ts b/gitnexus/src/core/group/extractors/grpc-extractor.ts
index 4d7ad7932..c08ba7c36 100644
--- a/gitnexus/src/core/group/extractors/grpc-extractor.ts
+++ b/gitnexus/src/core/group/extractors/grpc-extractor.ts
@@ -5,6 +5,7 @@ import { createIgnoreFilter } from '../../../config/ignore-service.js';
 import type { ContractExtractor, CypherExecutor } from '../contract-extractor.js';
 import type { ExtractedContract, RepoHandle } from '../types.js';
 import { readSafe } from './fs-utils.js';
+import { logger } from '../../logger.js';
 import {
   GRPC_SCAN_GLOB,
   getPluginForFile,
@@ -344,8 +345,7 @@ export function resolveProtoConflict(
   // services under a fabricated package-qualified contract id.
   if (winners.length !== 1) {
     const paths = candidates.map((c) => c.protoPath).join(', ');
-    // eslint-disable-next-line no-console -- TODO(pino-migration)
-    console.warn(
+    logger.warn(
       `[grpc-extractor] Ambiguous proto resolution for service "${serviceName}" from ${sourceFilePath}: ${winners.length} candidates tied at score ${maxScore} among [${paths}] — skipping canonical contract`,
     );
     return null;
diff --git a/gitnexus/src/core/group/extractors/java-workspace-extractor.ts b/gitnexus/src/core/group/extractors/java-workspace-extractor.ts
index 828e729ab..b6beed71c 100644
--- a/gitnexus/src/core/group/extractors/java-workspace-extractor.ts
+++ b/gitnexus/src/core/group/extractors/java-workspace-extractor.ts
@@ -4,6 +4,7 @@ import type { CypherExecutor } from '../contract-extractor.js';
 import type { GroupManifestLink, ContractRole } from '../types.js';
 import { shouldIgnorePath, loadIgnoreRules } from '../../../config/ignore-service.js';
 
+import { logger } from '../../logger.js';
 interface JavaProjectMeta {
   groupId: string;
   artifactId: string;
@@ -213,8 +214,7 @@ export async function extractJavaWorkspaceLinks(
     };
     const existing = projectsByKey.get(key);
     if (existing) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(
+      logger.warn(
         `[java-workspace-extractor] duplicate artifact "${key}" in "${groupPath}" and "${existing.groupPath}" — skipping "${groupPath}"`,
       );
       continue;
diff --git a/gitnexus/src/core/group/extractors/manifest-extractor.ts b/gitnexus/src/core/group/extractors/manifest-extractor.ts
index bba74f554..ab9c97960 100644
--- a/gitnexus/src/core/group/extractors/manifest-extractor.ts
+++ b/gitnexus/src/core/group/extractors/manifest-extractor.ts
@@ -1,6 +1,7 @@
 import type { ContractType, CrossLink, GroupManifestLink, StoredContract } from '../types.js';
 import type { CypherExecutor } from '../contract-extractor.js';
 
+import { logger } from '../../logger.js';
 export interface ManifestExtractResult {
   contracts: StoredContract[];
   crossLinks: CrossLink[];
@@ -298,8 +299,7 @@ export class ManifestExtractor {
       // fail the whole manifest extraction. Unresolved contracts still
       // get a synthetic symbolUid below, so cross-impact can proceed.
       const message = err instanceof Error ? err.message : String(err);
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(
+      logger.warn(
         `[manifest-extractor] resolveSymbol failed for ${link.type}:${link.contract} ` +
           `in ${repoPathKey}: ${message}`,
       );
diff --git a/gitnexus/src/core/group/extractors/node-workspace-extractor.ts b/gitnexus/src/core/group/extractors/node-workspace-extractor.ts
index 8e8c7dc89..aa40ac088 100644
--- a/gitnexus/src/core/group/extractors/node-workspace-extractor.ts
+++ b/gitnexus/src/core/group/extractors/node-workspace-extractor.ts
@@ -4,6 +4,7 @@ import type { CypherExecutor } from '../contract-extractor.js';
 import type { GroupManifestLink, ContractRole } from '../types.js';
 import { shouldIgnorePath, loadIgnoreRules } from '../../../config/ignore-service.js';
 
+import { logger } from '../../logger.js';
 interface PackageMeta {
   name: string;
   groupPath: string;
@@ -205,8 +206,7 @@ export async function extractNodeWorkspaceLinks(
     };
     const existing = packagesByName.get(manifest.name);
     if (existing) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(
+      logger.warn(
         `[node-workspace-extractor] duplicate package name "${manifest.name}" in "${groupPath}" and "${existing.groupPath}" — skipping "${groupPath}"`,
       );
       continue;
diff --git a/gitnexus/src/core/group/extractors/python-workspace-extractor.ts b/gitnexus/src/core/group/extractors/python-workspace-extractor.ts
index ccb3cd9f5..4453852a6 100644
--- a/gitnexus/src/core/group/extractors/python-workspace-extractor.ts
+++ b/gitnexus/src/core/group/extractors/python-workspace-extractor.ts
@@ -4,6 +4,7 @@ import type { CypherExecutor } from '../contract-extractor.js';
 import type { GroupManifestLink, ContractRole } from '../types.js';
 import { shouldIgnorePath, loadIgnoreRules } from '../../../config/ignore-service.js';
 
+import { logger } from '../../logger.js';
 interface PythonPackageMeta {
   name: string;
   importName: string;
@@ -204,8 +205,7 @@ export async function extractPythonWorkspaceLinks(
     };
     const existing = packagesByImportName.get(manifest.importName);
     if (existing) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(
+      logger.warn(
         `[python-workspace-extractor] duplicate package "${manifest.name}" in "${groupPath}" and "${existing.groupPath}" — skipping "${groupPath}"`,
       );
       continue;
diff --git a/gitnexus/src/core/group/extractors/rust-workspace-extractor.ts b/gitnexus/src/core/group/extractors/rust-workspace-extractor.ts
index 29efb12f5..63fe7ea82 100644
--- a/gitnexus/src/core/group/extractors/rust-workspace-extractor.ts
+++ b/gitnexus/src/core/group/extractors/rust-workspace-extractor.ts
@@ -5,6 +5,7 @@ import type { GroupManifestLink, ContractRole } from '../types.js';
 import { shouldIgnorePath } from '../../../config/ignore-service.js';
 import { loadIgnoreRules } from '../../../config/ignore-service.js';
 
+import { logger } from '../../logger.js';
 /**
  * Discover cross-crate contracts in a Rust workspace by reading each
  * member's `Cargo.toml` dependencies and scanning source files for
@@ -224,8 +225,7 @@ export async function extractRustWorkspaceLinks(
     };
     const existing = cratesByName.get(manifest.name);
     if (existing) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(
+      logger.warn(
         `[rust-workspace-extractor] duplicate crate name "${manifest.name}" in "${groupPath}" and "${existing.groupPath}" — skipping "${groupPath}"`,
       );
       continue;
diff --git a/gitnexus/src/core/group/service.ts b/gitnexus/src/core/group/service.ts
index dc942c7e5..de324e70b 100644
--- a/gitnexus/src/core/group/service.ts
+++ b/gitnexus/src/core/group/service.ts
@@ -14,6 +14,7 @@ import {
 } from './group-path-utils.js';
 import { getDefaultGitnexusDir, getGroupDir, listGroups, readContractRegistry } from './storage.js';
 import { syncGroup } from './sync.js';
+import { logger } from '../logger.js';
 import type {
   ContractRegistry,
   CrossLink,
@@ -170,13 +171,11 @@ async function loadContractRegistryResilient(
           contracts.push(row);
         } else {
           skippedCorrupt++;
-          // eslint-disable-next-line no-console -- TODO(pino-migration)
-          console.warn('[group] skipping corrupt contract row in contracts.json');
+          logger.warn('[group] skipping corrupt contract row in contracts.json');
         }
       } catch {
         skippedCorrupt++;
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.warn('[group] skipping corrupt contract row in contracts.json');
+        logger.warn('[group] skipping corrupt contract row in contracts.json');
       }
     }
   }
@@ -189,13 +188,11 @@ async function loadContractRegistryResilient(
           crossLinks.push(row);
         } else {
           skippedCorrupt++;
-          // eslint-disable-next-line no-console -- TODO(pino-migration)
-          console.warn('[group] skipping corrupt crossLinks row in contracts.json');
+          logger.warn('[group] skipping corrupt crossLinks row in contracts.json');
         }
       } catch {
         skippedCorrupt++;
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.warn('[group] skipping corrupt crossLinks row in contracts.json');
+        logger.warn('[group] skipping corrupt crossLinks row in contracts.json');
       }
     }
   }
diff --git a/gitnexus/src/core/group/sync.ts b/gitnexus/src/core/group/sync.ts
index 4a2373f2b..48b367647 100644
--- a/gitnexus/src/core/group/sync.ts
+++ b/gitnexus/src/core/group/sync.ts
@@ -15,6 +15,7 @@ import type { CypherExecutor } from './contract-extractor.js';
 import { writeContractRegistry } from './storage.js';
 import type { ContractRegistry } from './types.js';
 
+import { logger } from '../logger.js';
 export interface SyncOptions {
   extractorOverride?:
     | ((repo: RepoHandle) => Promise<StoredContract[]>)
@@ -198,8 +199,7 @@ export async function syncGroup(config: GroupConfig, opts?: SyncOptions): Promis
       allLinks = [...allLinks, ...wsResult.links];
       if (opts?.verbose) {
         for (const s of wsResult.stats) {
-          // eslint-disable-next-line no-console -- TODO(pino-migration)
-          console.log(
+          logger.info(
             `  workspace-deps: discovered ${s.linkCount} cross-${s.ecosystem.toLowerCase()} links from ${s.projectCount} ${s.ecosystem} projects`,
           );
         }
@@ -218,8 +218,7 @@ export async function syncGroup(config: GroupConfig, opts?: SyncOptions): Promis
     for (const link of allLinks) {
       const dangling = [link.from, link.to].filter((r) => !knownRepos.has(r));
       if (dangling.length > 0) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.warn(
+        logger.warn(
           `[group/sync] manifest link ${link.type}:${link.contract} references repos not in config.repos: ${dangling.join(', ')} — cross-links will use synthetic UIDs`,
         );
       }
@@ -230,8 +229,7 @@ export async function syncGroup(config: GroupConfig, opts?: SyncOptions): Promis
     autoContracts.push(...manifestResult.contracts);
     manifestCrossLinks = manifestResult.crossLinks;
     if (opts?.verbose) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.log(
+      logger.info(
         `  manifest: ${manifestCrossLinks.length} cross-links from ${allLinks.length} links (${config.links.length} declared + ${allLinks.length - config.links.length} discovered)`,
       );
     }
diff --git a/gitnexus/src/core/ingestion/ast-cache.ts b/gitnexus/src/core/ingestion/ast-cache.ts
index 69723abce..454c60df2 100644
--- a/gitnexus/src/core/ingestion/ast-cache.ts
+++ b/gitnexus/src/core/ingestion/ast-cache.ts
@@ -1,6 +1,7 @@
 import { LRUCache } from 'lru-cache';
 import Parser from 'tree-sitter';
 
+import { logger } from '../logger.js';
 /**
  * Minimal structural shape consumers need when reading Trees back
  * through a phase-dependency boundary. Declared here so phases that
@@ -49,8 +50,7 @@ export const createASTCache = (maxSize: number = 50): ASTCache => {
         // will hand freed memory to scope-resolution.
         (tree as unknown as { delete?: () => void }).delete?.();
       } catch (e) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.warn('Failed to delete tree from WASM memory', e);
+        logger.warn({ e }, 'Failed to delete tree from WASM memory');
       }
     },
   });
diff --git a/gitnexus/src/core/ingestion/call-processor.ts b/gitnexus/src/core/ingestion/call-processor.ts
index 203b14ede..6c59578b0 100644
--- a/gitnexus/src/core/ingestion/call-processor.ts
+++ b/gitnexus/src/core/ingestion/call-processor.ts
@@ -75,6 +75,7 @@ import { extractReturnTypeName, stripNullable } from './type-extractors/shared.j
 import type { LiteralTypeInferrer } from './type-extractors/types.js';
 import type { SyntaxNode } from './utils/ast-helpers.js';
 
+import { logger } from '../logger.js';
 /** Per-file resolved type bindings for exported symbols.
  *  Populated during call processing, consumed by Phase 14 re-resolution pass. */
 export type ExportedTypeMap = Map<string, Map<string, string>>;
@@ -784,8 +785,7 @@ export const processCalls = async (
       const query = new Parser.Query(lang, queryStr);
       matches = query.matches(tree.rootNode);
     } catch (queryError) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(`Query error for ${file.path}:`, queryError);
+      logger.warn({ queryError }, `Query error for ${file.path}:`);
       continue;
     }
 
@@ -1392,8 +1392,7 @@ export const processCalls = async (
 
   if (skippedByLang && skippedByLang.size > 0) {
     for (const [lang, count] of skippedByLang.entries()) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(
+      logger.warn(
         `[ingestion] Skipped ${count} ${lang} file(s) in call processing — ${lang} parser not available.`,
       );
     }
diff --git a/gitnexus/src/core/ingestion/cluster-enricher.ts b/gitnexus/src/core/ingestion/cluster-enricher.ts
index f1291cb8b..06cd4d0cd 100644
--- a/gitnexus/src/core/ingestion/cluster-enricher.ts
+++ b/gitnexus/src/core/ingestion/cluster-enricher.ts
@@ -7,6 +7,7 @@
 
 import { CommunityNode } from './community-processor.js';
 
+import { logger } from '../logger.js';
 // ============================================================================
 // TYPES
 // ============================================================================
@@ -128,8 +129,7 @@ export const enrichClusters = async (
       enrichments.set(community.id, enrichment);
     } catch (error) {
       // On error, fallback to heuristic
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(`Failed to enrich cluster ${community.id}:`, error);
+      logger.warn({ error }, `Failed to enrich cluster ${community.id}:`);
       enrichments.set(community.id, {
         name: community.heuristicLabel,
         keywords: [],
@@ -211,8 +211,7 @@ Output JSON array:
         }
       }
     } catch (error) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn('Batch enrichment failed, falling back to heuristics:', error);
+      logger.warn({ error }, 'Batch enrichment failed, falling back to heuristics:');
       // Fallback for this batch
       for (const community of batch) {
         enrichments.set(community.id, {
diff --git a/gitnexus/src/core/ingestion/cobol/cobol-copy-expander.ts b/gitnexus/src/core/ingestion/cobol/cobol-copy-expander.ts
index 156dc4a96..dda135b12 100644
--- a/gitnexus/src/core/ingestion/cobol/cobol-copy-expander.ts
+++ b/gitnexus/src/core/ingestion/cobol/cobol-copy-expander.ts
@@ -1,3 +1,4 @@
+import { logger } from '../../logger.js';
 /**
  * COBOL COPY statement expansion engine.
  *
@@ -454,8 +455,7 @@ export function expandCopies(
       if (visited.has(resolvedPath)) {
         if (!warnedCircular.has(resolvedPath)) {
           warnedCircular.add(resolvedPath);
-          // eslint-disable-next-line no-console -- TODO(pino-migration)
-          console.warn(
+          logger.warn(
             `[cobol-copy-expander] Circular COPY detected: ${cs.target} (${resolvedPath}) ` +
               `includes itself. Skipping expansion.`,
           );
@@ -465,8 +465,7 @@ export function expandCopies(
 
       // Max depth exceeded — keep unexpanded
       if (depth >= maxDepth) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.warn(
+        logger.warn(
           `[cobol-copy-expander] Max expansion depth (${maxDepth}) reached for ` +
             `COPY ${cs.target} in ${srcPath}. Skipping expansion.`,
         );
@@ -477,8 +476,7 @@ export function expandCopies(
       if (++totalExpansions > MAX_TOTAL_EXPANSIONS) {
         if (!warnedCircular.has('__max_total__')) {
           warnedCircular.add('__max_total__');
-          // eslint-disable-next-line no-console -- TODO(pino-migration)
-          console.warn(
+          logger.warn(
             `[cobol-copy-expander] Max total expansions (${MAX_TOTAL_EXPANSIONS}) reached ` +
               `in ${srcPath}. Skipping further expansions.`,
           );
diff --git a/gitnexus/src/core/ingestion/filesystem-walker.ts b/gitnexus/src/core/ingestion/filesystem-walker.ts
index 81ea95b95..4d6725e24 100644
--- a/gitnexus/src/core/ingestion/filesystem-walker.ts
+++ b/gitnexus/src/core/ingestion/filesystem-walker.ts
@@ -5,6 +5,7 @@ import path from 'path';
 import { glob } from 'glob';
 import { createIgnoreFilter } from '../../config/ignore-service.js';
 
+import { logger } from '../logger.js';
 export interface FileEntry {
   path: string;
   content: string;
@@ -74,12 +75,10 @@ export const walkRepositoryPaths = async (
   if (skippedLarge > 0) {
     const isDefault = maxFileSizeBytes === DEFAULT_MAX_FILE_SIZE_BYTES;
     const suffix = isDefault ? ', likely generated/vendored' : '';
-    // eslint-disable-next-line no-console -- TODO(pino-migration)
-    console.warn(`  Skipped ${skippedLarge} large files (>${maxFileSizeBytes / 1024}KB${suffix})`);
+    logger.warn(`  Skipped ${skippedLarge} large files (>${maxFileSizeBytes / 1024}KB${suffix})`);
     if (isVerboseIngestionEnabled()) {
       for (const p of skippedLargePaths) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.warn(`  - ${p}`);
+        logger.warn(`  - ${p}`);
       }
     }
   }
diff --git a/gitnexus/src/core/ingestion/heritage-processor.ts b/gitnexus/src/core/ingestion/heritage-processor.ts
index 8e4de1bf2..2c973ad8e 100644
--- a/gitnexus/src/core/ingestion/heritage-processor.ts
+++ b/gitnexus/src/core/ingestion/heritage-processor.ts
@@ -34,6 +34,7 @@ import type { ResolutionContext } from './model/resolution-context.js';
 import { TIER_CONFIDENCE } from './model/resolution-context.js';
 import type { HeritageInfo } from './heritage-types.js';
 
+import { logger } from '../logger.js';
 /**
  * Derive the heritage-resolution strategy for a language from its
  * `LanguageProvider`. This is the production wiring that `buildHeritageMap`
@@ -237,8 +238,7 @@ export const processHeritage = async (
       query = new Parser.Query(treeSitterLang, queryStr);
       matches = query.matches(tree.rootNode);
     } catch (queryError) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(`Heritage query error for ${file.path}:`, queryError);
+      logger.warn({ queryError }, `Heritage query error for ${file.path}:`);
       continue;
     }
 
@@ -268,8 +268,7 @@ export const processHeritage = async (
 
   if (skippedByLang && skippedByLang.size > 0) {
     for (const [lang, count] of skippedByLang.entries()) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(
+      logger.warn(
         `[ingestion] Skipped ${count} ${lang} file(s) in heritage processing — ${lang} parser not available.`,
       );
     }
diff --git a/gitnexus/src/core/ingestion/import-processor.ts b/gitnexus/src/core/ingestion/import-processor.ts
index a8bcf2a69..03cbed5b7 100644
--- a/gitnexus/src/core/ingestion/import-processor.ts
+++ b/gitnexus/src/core/ingestion/import-processor.ts
@@ -27,6 +27,7 @@ import type { SyntaxNode } from './utils/ast-helpers.js';
 import { isDev } from './utils/env.js';
 import { isRegistryPrimary } from './registry-primary-flag.js';
 
+import { logger } from '../logger.js';
 // Type: Map<FilePath, Set<ResolvedFilePath>>
 // Stores all files that a given file imports from
 export type ImportMap = Map<string, Set<string>>;
@@ -324,22 +325,18 @@ export const processImports = async (
       matches = query.matches(tree.rootNode);
     } catch (queryError: any) {
       if (isDev) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.group(`🔴 Query Error: ${file.path}`);
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.log('Language:', language);
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.log('Query (first 200 chars):', queryStr.substring(0, 200) + '...');
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.log('Error:', queryError?.message || queryError);
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.log('File content (first 300 chars):', file.content.substring(0, 300));
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.log('AST root type:', tree.rootNode?.type);
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.log('AST has errors:', tree.rootNode?.hasError);
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.groupEnd();
+        logger.error(
+          {
+            file: file.path,
+            language,
+            err: queryError?.message || queryError,
+            queryPreview: queryStr.substring(0, 200) + '...',
+            contentPreview: file.content.substring(0, 300),
+            astRootType: tree.rootNode?.type,
+            astHasError: tree.rootNode?.hasError,
+          },
+          'tree-sitter query error',
+        );
       }
 
       if (wasReparsed) (tree as unknown as { delete?: () => void }).delete?.();
@@ -354,8 +351,7 @@ export const processImports = async (
         const sourceNode = captureMap['import.source'];
         if (!sourceNode) {
           if (isDev) {
-            // eslint-disable-next-line no-console -- TODO(pino-migration)
-            console.log(`⚠️ Import captured but no source node in ${file.path}`);
+            logger.info(`⚠️ Import captured but no source node in ${file.path}`);
           }
           return;
         }
@@ -408,16 +404,14 @@ export const processImports = async (
 
   if (skippedByLang && skippedByLang.size > 0) {
     for (const [lang, count] of skippedByLang.entries()) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(
+      logger.warn(
         `[ingestion] Skipped ${count} ${lang} file(s) in import processing — ${lang} parser not available.`,
       );
     }
   }
 
   if (isDev) {
-    // eslint-disable-next-line no-console -- TODO(pino-migration)
-    console.log(
+    logger.info(
       `📊 Import processing complete: ${getResolvedCount()}/${totalImportsFound} imports resolved to graph edges`,
     );
   }
@@ -509,8 +503,7 @@ export const processImportsFromExtracted = async (
   );
 
   if (isDev) {
-    // eslint-disable-next-line no-console -- TODO(pino-migration)
-    console.log(
+    logger.info(
       `📊 Import processing (fast path): ${getResolvedCount()}/${totalImportsFound} imports resolved to graph edges`,
     );
   }
diff --git a/gitnexus/src/core/ingestion/language-config.ts b/gitnexus/src/core/ingestion/language-config.ts
index a14a0d2ab..f51ef57c6 100644
--- a/gitnexus/src/core/ingestion/language-config.ts
+++ b/gitnexus/src/core/ingestion/language-config.ts
@@ -4,6 +4,7 @@ import type { ImportConfigs } from './import-resolvers/types.js';
 
 import { isDev } from './utils/env.js';
 
+import { logger } from '../logger.js';
 // ============================================================================
 // LANGUAGE-SPECIFIC CONFIG TYPES
 // ============================================================================
@@ -82,8 +83,7 @@ export async function loadTsconfigPaths(repoRoot: string): Promise<TsconfigPaths
 
       if (aliases.size > 0) {
         if (isDev) {
-          // eslint-disable-next-line no-console -- TODO(pino-migration)
-          console.log(`📦 Loaded ${aliases.size} path aliases from ${filename}`);
+          logger.info(`📦 Loaded ${aliases.size} path aliases from ${filename}`);
         }
         return { aliases, baseUrl };
       }
@@ -105,8 +105,7 @@ export async function loadGoModulePath(repoRoot: string): Promise<GoModuleConfig
     const match = content.match(/^module\s+(\S+)/m);
     if (match) {
       if (isDev) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.log(`📦 Loaded Go module path: ${match[1]}`);
+        logger.info(`📦 Loaded Go module path: ${match[1]}`);
       }
       return { modulePath: match[1] };
     }
@@ -134,8 +133,7 @@ export async function loadComposerConfig(repoRoot: string): Promise<ComposerConf
     }
 
     if (isDev) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.log(`📦 Loaded ${psr4.size} PSR-4 mappings from composer.json`);
+      logger.info(`📦 Loaded ${psr4.size} PSR-4 mappings from composer.json`);
     }
     return { psr4 };
   } catch {
@@ -181,8 +179,7 @@ export async function loadCSharpProjectConfig(repoRoot: string): Promise<CSharpP
             const projectDir = path.relative(repoRoot, dir).replace(/\\/g, '/');
             configs.push({ rootNamespace, projectDir });
             if (isDev) {
-              // eslint-disable-next-line no-console -- TODO(pino-migration)
-              console.log(
+              logger.info(
                 `📦 Loaded C# project: ${entry.name} (namespace: ${rootNamespace}, dir: ${projectDir})`,
               );
             }
@@ -221,8 +218,7 @@ export async function loadSwiftPackageConfig(repoRoot: string): Promise<SwiftPac
 
   if (targets.size > 0) {
     if (isDev) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.log(`📦 Loaded ${targets.size} Swift package targets`);
+      logger.info(`📦 Loaded ${targets.size} Swift package targets`);
     }
     return { targets };
   }
diff --git a/gitnexus/src/core/ingestion/method-extractors/generic.ts b/gitnexus/src/core/ingestion/method-extractors/generic.ts
index 886f0756d..f02faef35 100644
--- a/gitnexus/src/core/ingestion/method-extractors/generic.ts
+++ b/gitnexus/src/core/ingestion/method-extractors/generic.ts
@@ -8,6 +8,7 @@
  */
 
 import type { SyntaxNode } from '../utils/ast-helpers.js';
+import { logger } from '../../logger.js';
 import type {
   MethodExtractor,
   MethodExtractorContext,
@@ -158,8 +159,7 @@ function findBodies(node: SyntaxNode, bodyNodeSet: Set<string>): SyntaxNode[] {
     // Fallback: body field exists but its type is not in bodyNodeTypes.
     // This may indicate a config typo — log for debugging if NODE_ENV is development.
     if (process.env.NODE_ENV === 'development') {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(
+      logger.warn(
         `[MethodExtractor] body field type '${bodyField.type}' not in bodyNodeTypes for node '${node.type}'`,
       );
     }
diff --git a/gitnexus/src/core/ingestion/parsing-processor.ts b/gitnexus/src/core/ingestion/parsing-processor.ts
index e7191e554..8803ec023 100644
--- a/gitnexus/src/core/ingestion/parsing-processor.ts
+++ b/gitnexus/src/core/ingestion/parsing-processor.ts
@@ -34,6 +34,7 @@ import {
 import type { LanguageProvider } from './language-provider.js';
 import type { ParsedFile } from 'gitnexus-shared';
 import { WorkerPool } from './workers/worker-pool.js';
+import { logger } from '../logger.js';
 import type {
   ParseWorkerResult,
   ParseWorkerInput,
@@ -191,8 +192,7 @@ const processParsingWithWorkers = async (
     const summary = Array.from(skippedLanguages.entries())
       .map(([lang, count]) => `${lang}: ${count}`)
       .join(', ');
-    // eslint-disable-next-line no-console -- TODO(pino-migration)
-    console.warn(`  Skipped unsupported languages: ${summary}`);
+    logger.warn(`  Skipped unsupported languages: ${summary}`);
   }
 
   // Final progress
@@ -383,8 +383,7 @@ const processParsingSequential = async (
         bufferSize: getTreeSitterBufferSize(parseContent),
       });
     } catch (parseError) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(`Skipping unparseable file: ${file.path}`);
+      logger.warn(`Skipping unparseable file: ${file.path}`);
       continue;
     }
 
@@ -410,8 +409,7 @@ const processParsingSequential = async (
       query = new Parser.Query(language, queryString);
       matches = query.matches(tree.rootNode);
     } catch (queryError) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(`Query error for ${file.path}:`, queryError);
+      logger.warn({ queryError }, `Query error for ${file.path}:`);
       continue;
     }
 
@@ -704,8 +702,7 @@ const processParsingSequential = async (
 
   if (skippedByLang && skippedByLang.size > 0) {
     for (const [lang, count] of skippedByLang.entries()) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(
+      logger.warn(
         `[ingestion] Skipped ${count} ${lang} file(s) in parsing processing — ${lang} parser not available.`,
       );
     }
@@ -746,8 +743,7 @@ export const processParsing = async (
       // in scope-resolution with an empty cache and get re-parsed.
       // Surfacing this in PROF mode prevents silent perf cliffs when
       // a repo crosses the worker-pool threshold.
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(
+      logger.warn(
         `[scope-resolution prof] worker pool engaged for ${files.length} files — cross-phase tree cache will be empty; scope-resolution re-parses.`,
       );
     }
@@ -762,8 +758,7 @@ export const processParsing = async (
       );
     } catch (err) {
       const message = err instanceof Error ? err.message : String(err);
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn('Worker pool parsing stopped; continuing with sequential parser:', message);
+      logger.warn({ message }, 'Worker pool parsing stopped; continuing with sequential parser:');
       reportProgress?.(
         lastProgress,
         files.length,
diff --git a/gitnexus/src/core/ingestion/pipeline-phases/cobol.ts b/gitnexus/src/core/ingestion/pipeline-phases/cobol.ts
index 2ead44be3..c9332aabc 100644
--- a/gitnexus/src/core/ingestion/pipeline-phases/cobol.ts
+++ b/gitnexus/src/core/ingestion/pipeline-phases/cobol.ts
@@ -15,6 +15,7 @@ import { readFileContents } from '../filesystem-walker.js';
 import type { StructureOutput } from './structure.js';
 import { isDev } from '../utils/env.js';
 
+import { logger } from '../../logger.js';
 export interface CobolOutput {
   programs: number;
   paragraphs: number;
@@ -47,8 +48,7 @@ export const cobolPhase: PipelinePhase<CobolOutput> = {
     const cobolResult = processCobol(ctx.graph, cobolFiles, allPathSet);
 
     if (isDev) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.log(
+      logger.info(
         `  COBOL: ${cobolResult.programs} programs, ${cobolResult.paragraphs} paragraphs, ${cobolResult.sections} sections from ${cobolFiles.length} files`,
       );
       if (
@@ -56,14 +56,12 @@ export const cobolPhase: PipelinePhase<CobolOutput> = {
         cobolResult.execCicsBlocks > 0 ||
         cobolResult.entryPoints > 0
       ) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.log(
+        logger.info(
           `  COBOL enriched: ${cobolResult.execSqlBlocks} SQL blocks, ${cobolResult.execCicsBlocks} CICS blocks, ${cobolResult.entryPoints} entry points, ${cobolResult.moves} moves, ${cobolResult.fileDeclarations} file declarations`,
         );
       }
       if (cobolResult.jclJobs > 0) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.log(`  JCL: ${cobolResult.jclJobs} jobs, ${cobolResult.jclSteps} steps`);
+        logger.info(`  JCL: ${cobolResult.jclJobs} jobs, ${cobolResult.jclSteps} steps`);
       }
     }
 
diff --git a/gitnexus/src/core/ingestion/pipeline-phases/communities.ts b/gitnexus/src/core/ingestion/pipeline-phases/communities.ts
index d68821871..0e29b6cc2 100644
--- a/gitnexus/src/core/ingestion/pipeline-phases/communities.ts
+++ b/gitnexus/src/core/ingestion/pipeline-phases/communities.ts
@@ -15,6 +15,7 @@ import type { StructureOutput } from './structure.js';
 import { processCommunities, type CommunityDetectionResult } from '../community-processor.js';
 import { isDev } from '../utils/env.js';
 
+import { logger } from '../../logger.js';
 export interface CommunitiesOutput {
   communityResult: CommunityDetectionResult;
 }
@@ -47,8 +48,7 @@ export const communitiesPhase: PipelinePhase<CommunitiesOutput> = {
     });
 
     if (isDev) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.log(
+      logger.info(
         `🏘️ Community detection: ${communityResult.stats.totalCommunities} communities found (modularity: ${communityResult.stats.modularity.toFixed(3)})`,
       );
     }
diff --git a/gitnexus/src/core/ingestion/pipeline-phases/cross-file-impl.ts b/gitnexus/src/core/ingestion/pipeline-phases/cross-file-impl.ts
index a8dd94d44..5c014ed73 100644
--- a/gitnexus/src/core/ingestion/pipeline-phases/cross-file-impl.ts
+++ b/gitnexus/src/core/ingestion/pipeline-phases/cross-file-impl.ts
@@ -23,6 +23,7 @@ import { topologicalLevelSort } from '../utils/graph-sort.js';
 import type { KnowledgeGraph } from '../../graph/types.js';
 import { isDev } from '../utils/env.js';
 
+import { logger } from '../../logger.js';
 /** Max AST trees to keep in LRU cache for cross-file binding propagation. */
 const AST_CACHE_CAP = 50;
 
@@ -60,8 +61,7 @@ export async function runCrossFileBindingPropagation(
   const { levels, cycleCount } = topologicalLevelSort(ctx.importMap);
 
   if (isDev && cycleCount > 0) {
-    // eslint-disable-next-line no-console -- TODO(pino-migration)
-    console.log(`🔄 ${cycleCount} files in import cycles (processed last in undefined order)`);
+    logger.info(`🔄 ${cycleCount} files in import cycles (processed last in undefined order)`);
   }
 
   let filesWithGaps = 0;
@@ -89,8 +89,7 @@ export async function runCrossFileBindingPropagation(
   const gapRatio = totalFiles > 0 ? filesWithGaps / totalFiles : 0;
   if (gapRatio < CROSS_FILE_SKIP_THRESHOLD && filesWithGaps < gapThreshold) {
     if (isDev) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.log(
+      logger.info(
         `⏭️ Cross-file re-resolution skipped (${filesWithGaps}/${totalFiles} files, ${(gapRatio * 100).toFixed(1)}% < ${CROSS_FILE_SKIP_THRESHOLD * 100}% threshold)`,
       );
     }
@@ -195,8 +194,7 @@ export async function runCrossFileBindingPropagation(
 
     if (crossFileResolved >= MAX_CROSS_FILE_REPROCESS) {
       if (isDev)
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.log(`⚠️ Cross-file re-resolution capped at ${MAX_CROSS_FILE_REPROCESS} files`);
+        logger.info(`⚠️ Cross-file re-resolution capped at ${MAX_CROSS_FILE_REPROCESS} files`);
       break;
     }
   }
@@ -207,8 +205,7 @@ export async function runCrossFileBindingPropagation(
     const elapsed = Date.now() - crossFileStart;
     const totalElapsed = Date.now() - pipelineStart;
     const reResolutionPct = totalElapsed > 0 ? ((elapsed / totalElapsed) * 100).toFixed(1) : '0';
-    // eslint-disable-next-line no-console -- TODO(pino-migration)
-    console.log(
+    logger.info(
       `🔗 Cross-file re-resolution: ${crossFileResolved} candidates re-processed` +
         ` in ${elapsed}ms (${reResolutionPct}% of total ingestion time so far)`,
     );
diff --git a/gitnexus/src/core/ingestion/pipeline-phases/cross-file.ts b/gitnexus/src/core/ingestion/pipeline-phases/cross-file.ts
index ac3ee54c7..3ea604b4d 100644
--- a/gitnexus/src/core/ingestion/pipeline-phases/cross-file.ts
+++ b/gitnexus/src/core/ingestion/pipeline-phases/cross-file.ts
@@ -36,6 +36,7 @@ import type { ParseOutput } from './parse.js';
 import { runCrossFileBindingPropagation } from './cross-file-impl.js';
 import { isDev } from '../utils/env.js';
 
+import { logger } from '../../logger.js';
 export interface CrossFileOutput {
   /** Number of files re-processed during cross-file propagation. */
   filesReprocessed: number;
@@ -59,13 +60,11 @@ export const crossFilePhase: PipelinePhase<CrossFileOutput> = {
       if (isDev) {
         if (bindingAccumulator.totalBindings > 0) {
           const memKB = Math.round(bindingAccumulator.estimateMemoryBytes() / 1024);
-          // eslint-disable-next-line no-console -- TODO(pino-migration)
-          console.log(
+          logger.info(
             `📦 BindingAccumulator: ${bindingAccumulator.totalBindings} bindings across ${bindingAccumulator.fileCount} files (~${memKB} KB)`,
           );
         } else if (totalFiles > 0) {
-          // eslint-disable-next-line no-console -- TODO(pino-migration)
-          console.log(
+          logger.info(
             `📦 BindingAccumulator: EMPTY — 0 bindings across 0 files despite ${totalFiles} parsed files. If the codebase has typed bindings, this indicates an upstream regression.`,
           );
         }
diff --git a/gitnexus/src/core/ingestion/pipeline-phases/markdown.ts b/gitnexus/src/core/ingestion/pipeline-phases/markdown.ts
index 43631a3a9..dd57518c1 100644
--- a/gitnexus/src/core/ingestion/pipeline-phases/markdown.ts
+++ b/gitnexus/src/core/ingestion/pipeline-phases/markdown.ts
@@ -15,6 +15,7 @@ import { readFileContents } from '../filesystem-walker.js';
 import type { StructureOutput } from './structure.js';
 import { isDev } from '../utils/env.js';
 
+import { logger } from '../../logger.js';
 export interface MarkdownOutput {
   /** Number of markdown sections extracted. */
   sections: number;
@@ -48,8 +49,7 @@ export const markdownPhase: PipelinePhase<MarkdownOutput> = {
     const mdResult = processMarkdown(ctx.graph, mdFiles, allPathSet);
 
     if (isDev) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.log(
+      logger.info(
         `  Markdown: ${mdResult.sections} sections, ${mdResult.links} cross-links from ${mdFiles.length} files`,
       );
     }
diff --git a/gitnexus/src/core/ingestion/pipeline-phases/mro.ts b/gitnexus/src/core/ingestion/pipeline-phases/mro.ts
index 9f5bbb0a2..c098f2b7b 100644
--- a/gitnexus/src/core/ingestion/pipeline-phases/mro.ts
+++ b/gitnexus/src/core/ingestion/pipeline-phases/mro.ts
@@ -15,6 +15,7 @@ import type { StructureOutput } from './structure.js';
 import { computeMRO } from '../mro-processor.js';
 import { isDev } from '../utils/env.js';
 
+import { logger } from '../../logger.js';
 export interface MROOutput {
   entries: number;
   ambiguityCount: number;
@@ -42,8 +43,7 @@ export const mroPhase: PipelinePhase<MROOutput> = {
     const mroResult = computeMRO(ctx.graph);
 
     if (isDev && mroResult.entries.length > 0) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.log(
+      logger.info(
         `🔀 MRO: ${mroResult.entries.length} classes analyzed, ${mroResult.ambiguityCount} ambiguities, ${mroResult.overrideEdges} METHOD_OVERRIDES, ${mroResult.methodImplementsEdges} METHOD_IMPLEMENTS`,
       );
     }
diff --git a/gitnexus/src/core/ingestion/pipeline-phases/orm.ts b/gitnexus/src/core/ingestion/pipeline-phases/orm.ts
index 2f6082f76..4e6021efa 100644
--- a/gitnexus/src/core/ingestion/pipeline-phases/orm.ts
+++ b/gitnexus/src/core/ingestion/pipeline-phases/orm.ts
@@ -16,6 +16,7 @@ import type { ExtractedORMQuery } from '../workers/parse-worker.js';
 import type { KnowledgeGraph } from '../../graph/types.js';
 import { isDev } from '../utils/env.js';
 
+import { logger } from '../../logger.js';
 export interface ORMOutput {
   edgesCreated: number;
   modelCount: number;
@@ -91,8 +92,7 @@ function processORMQueries(
   }
 
   if (isDev) {
-    // eslint-disable-next-line no-console -- TODO(pino-migration)
-    console.log(
+    logger.info(
       `ORM dataflow: ${edgesCreated} QUERIES edges, ${modelNodes.size} models (${queries.length} total calls)`,
     );
   }
diff --git a/gitnexus/src/core/ingestion/pipeline-phases/parse-impl.ts b/gitnexus/src/core/ingestion/pipeline-phases/parse-impl.ts
index b6f1c7047..bd39a4330 100644
--- a/gitnexus/src/core/ingestion/pipeline-phases/parse-impl.ts
+++ b/gitnexus/src/core/ingestion/pipeline-phases/parse-impl.ts
@@ -69,6 +69,7 @@ import { isDev } from '../utils/env.js';
 import { synthesizeWildcardImportBindings, needsSynthesis } from './wildcard-synthesis.js';
 import { extractORMQueriesInline } from './orm-extraction.js';
 
+import { logger } from '../../logger.js';
 // ── Constants ──────────────────────────────────────────────────────────────
 
 /** Max bytes of source content to load per parse chunk. */
@@ -136,8 +137,7 @@ export async function runChunkedParseAndResolve(
     }
   }
   for (const [lang, count] of skippedByLang) {
-    // eslint-disable-next-line no-console -- TODO(pino-migration)
-    console.warn(
+    logger.warn(
       `Skipping ${count} ${lang} file(s) — ${lang} parser not available (native binding may not have built). Try: npm rebuild tree-sitter-${lang}`,
     );
   }
@@ -172,8 +172,7 @@ export async function runChunkedParseAndResolve(
 
   if (isDev) {
     const totalMB = parseableScanned.reduce((s, f) => s + f.size, 0) / (1024 * 1024);
-    // eslint-disable-next-line no-console -- TODO(pino-migration)
-    console.log(
+    logger.info(
       `📂 Scan: ${totalFiles} paths, ${totalParseable} parseable (${totalMB.toFixed(0)}MB), ${numChunks} chunks @ ${CHUNK_BYTE_BUDGET / (1024 * 1024)}MB budget`,
     );
   }
@@ -222,10 +221,9 @@ export async function runChunkedParseAndResolve(
       }
       workerPool = createWorkerPool(workerUrl);
     } catch (err) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(
+      logger.warn(
+        { err: (err as Error).message },
         'Worker pool creation failed, using sequential fallback:',
-        (err as Error).message,
       );
     }
   }
@@ -342,8 +340,7 @@ export async function runChunkedParseAndResolve(
             exportedTypeMap,
           );
           if (isDev && enrichedCount > 0) {
-            // eslint-disable-next-line no-console -- TODO(pino-migration)
-            console.log(
+            logger.info(
               `🔗 E1: Seeded ${enrichedCount} cross-file receiver types (chunk ${chunkIdx + 1})`,
             );
           }
@@ -542,8 +539,7 @@ export async function runChunkedParseAndResolve(
       const rcStats = ctx.getStats();
       const total = rcStats.cacheHits + rcStats.cacheMisses;
       const hitRate = total > 0 ? ((rcStats.cacheHits / total) * 100).toFixed(1) : '0';
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.log(
+      logger.info(
         `🔍 Resolution cache: ${rcStats.cacheHits} hits, ${rcStats.cacheMisses} misses (${hitRate}% hit rate)`,
       );
     }
@@ -559,17 +555,15 @@ export async function runChunkedParseAndResolve(
       bindingAccumulator.finalize();
       const enriched = enrichExportedTypeMap(bindingAccumulator, graph, exportedTypeMap);
       if (isDev && enriched > 0) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.log(
+        logger.info(
           `🔗 Worker TypeEnv enrichment: ${enriched} fixpoint-inferred exports added to ExportedTypeMap`,
         );
       }
     } catch (enrichErr) {
       if (isDev) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.warn(
+        logger.warn(
+          { err: (enrichErr as Error).message },
           'Post-fallback finalize/enrich failed during cleanup:',
-          (enrichErr as Error).message,
         );
       }
     }
@@ -578,8 +572,7 @@ export async function runChunkedParseAndResolve(
   if (!hasSynthesized) {
     const synthesized = synthesizeWildcardImportBindings(graph, ctx);
     if (isDev && synthesized > 0) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.log(
+      logger.info(
         `🔗 Synthesized ${synthesized} additional wildcard import bindings (Go/Ruby/C++/Swift/Python)`,
       );
     }
diff --git a/gitnexus/src/core/ingestion/pipeline-phases/processes.ts b/gitnexus/src/core/ingestion/pipeline-phases/processes.ts
index 4358d24e5..166faea20 100644
--- a/gitnexus/src/core/ingestion/pipeline-phases/processes.ts
+++ b/gitnexus/src/core/ingestion/pipeline-phases/processes.ts
@@ -19,6 +19,7 @@ import { processProcesses, type ProcessDetectionResult } from '../process-proces
 import { generateId } from '../../../lib/utils.js';
 import { isDev } from '../utils/env.js';
 
+import { logger } from '../../logger.js';
 export interface ProcessesOutput {
   processResult: ProcessDetectionResult;
 }
@@ -67,8 +68,7 @@ export const processesPhase: PipelinePhase<ProcessesOutput> = {
     );
 
     if (isDev) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.log(
+      logger.info(
         `🔄 Process detection: ${processResult.stats.totalProcesses} processes found (${processResult.stats.crossCommunityCount} cross-community)`,
       );
     }
@@ -168,8 +168,7 @@ export const processesPhase: PipelinePhase<ProcessesOutput> = {
         }
       }
       if (isDev && linked > 0) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.log(`🔗 Linked ${linked} Route/Tool nodes to execution flows`);
+        logger.info(`🔗 Linked ${linked} Route/Tool nodes to execution flows`);
       }
     }
 
diff --git a/gitnexus/src/core/ingestion/pipeline-phases/routes.ts b/gitnexus/src/core/ingestion/pipeline-phases/routes.ts
index 3dc72c114..de3a8ddb8 100644
--- a/gitnexus/src/core/ingestion/pipeline-phases/routes.ts
+++ b/gitnexus/src/core/ingestion/pipeline-phases/routes.ts
@@ -32,6 +32,7 @@ import { generateId } from '../../../lib/utils.js';
 import { readFileContents } from '../filesystem-walker.js';
 import { isDev } from '../utils/env.js';
 
+import { logger } from '../../logger.js';
 const EXPO_NAV_PATTERNS = [
   /router\.(push|replace|navigate)\(\s*['"`]([^'"`]+)['"`]/g,
   /<Link\s+[^>]*href=\s*['"`]([^'"`]+)['"`]/g,
@@ -174,8 +175,7 @@ export const routesPhase: PipelinePhase<RoutesOutput> = {
       }
 
       if (isDev) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.log(
+        logger.info(
           `🗺️ Route registry: ${routeRegistry.size} routes${duplicateRoutes > 0 ? ` (${duplicateRoutes} duplicate URLs skipped)` : ''}`,
         );
       }
@@ -225,8 +225,7 @@ export const routesPhase: PipelinePhase<RoutesOutput> = {
             linkedCount++;
           }
           if (isDev && linkedCount > 0) {
-            // eslint-disable-next-line no-console -- TODO(pino-migration)
-            console.log(
+            logger.info(
               `🛡️ Linked ${mwPath} middleware [${mwLabel.join(', ')}] to ${linkedCount} routes`,
             );
           }
@@ -292,8 +291,7 @@ export const routesPhase: PipelinePhase<RoutesOutput> = {
 
       processNextjsFetchRoutes(ctx.graph, allFetchCalls, routeURLToFile, consumerContents);
       if (isDev) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.log(
+        logger.info(
           `🔗 Processed ${allFetchCalls.length} fetch() calls against ${routeRegistry.size} routes`,
         );
       }
diff --git a/gitnexus/src/core/ingestion/pipeline-phases/runner.ts b/gitnexus/src/core/ingestion/pipeline-phases/runner.ts
index d5c789e13..0bfc45bd4 100644
--- a/gitnexus/src/core/ingestion/pipeline-phases/runner.ts
+++ b/gitnexus/src/core/ingestion/pipeline-phases/runner.ts
@@ -15,6 +15,7 @@
 import type { PipelinePhase, PipelineContext, PhaseResult } from './types.js';
 import { isDev } from '../utils/env.js';
 
+import { logger } from '../../logger.js';
 /**
  * Validate that the phases form a valid dependency graph (no cycles, all deps present).
  * Returns phases in topological execution order.
@@ -176,8 +177,7 @@ export async function runPipeline(
     const start = Date.now();
 
     if (isDev) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.log(`▶ Phase: ${phase.name}`);
+      logger.info(`▶ Phase: ${phase.name}`);
     }
 
     // Only expose declared dependencies — prevents hidden coupling to undeclared phases.
@@ -221,8 +221,7 @@ export async function runPipeline(
     });
 
     if (isDev) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.log(`✓ Phase: ${phase.name} (${durationMs}ms)`);
+      logger.info(`✓ Phase: ${phase.name} (${durationMs}ms)`);
     }
   }
 
diff --git a/gitnexus/src/core/ingestion/pipeline-phases/tools.ts b/gitnexus/src/core/ingestion/pipeline-phases/tools.ts
index 053a5a6f0..32a0ae71f 100644
--- a/gitnexus/src/core/ingestion/pipeline-phases/tools.ts
+++ b/gitnexus/src/core/ingestion/pipeline-phases/tools.ts
@@ -16,6 +16,7 @@ import { generateId } from '../../../lib/utils.js';
 import { readFileContents } from '../filesystem-walker.js';
 import { isDev } from '../utils/env.js';
 
+import { logger } from '../../logger.js';
 export interface ToolDef {
   name: string;
   filePath: string;
@@ -104,8 +105,7 @@ export const toolsPhase: PipelinePhase<ToolsOutput> = {
       }
 
       if (isDev) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.log(`🔧 Tool registry: ${toolDefs.length} tools detected`);
+        logger.info(`🔧 Tool registry: ${toolDefs.length} tools detected`);
       }
     }
 
diff --git a/gitnexus/src/core/ingestion/process-processor.ts b/gitnexus/src/core/ingestion/process-processor.ts
index 10228008b..aa744e54d 100644
--- a/gitnexus/src/core/ingestion/process-processor.ts
+++ b/gitnexus/src/core/ingestion/process-processor.ts
@@ -17,6 +17,7 @@ import { calculateEntryPointScore, isTestFile } from './entry-point-scoring.js';
 import { SupportedLanguages } from 'gitnexus-shared';
 import { isDev } from './utils/env.js';
 
+import { logger } from '../logger.js';
 // ============================================================================
 // CONFIGURATION
 // ============================================================================
@@ -319,16 +320,13 @@ const findEntryPoints = (
 
   // DEBUG: Log top candidates with new scoring details
   if (sorted.length > 0 && isDev) {
-    // eslint-disable-next-line no-console -- TODO(pino-migration)
-    console.log(`[Process] Top 10 entry point candidates (new scoring):`);
+    logger.info(`[Process] Top 10 entry point candidates (new scoring):`);
     sorted.slice(0, 10).forEach((c, i) => {
       const node = graph.getNode(c.id);
       const exported = node?.properties.isExported ? '✓' : '✗';
       const shortPath = node?.properties.filePath?.split('/').slice(-2).join('/') || '';
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.log(`  ${i + 1}. ${node?.properties.name} [exported:${exported}] (${shortPath})`);
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.log(`     score: ${c.score.toFixed(2)} = [${c.reasons.join(' × ')}]`);
+      logger.info(`  ${i + 1}. ${node?.properties.name} [exported:${exported}] (${shortPath})`);
+      logger.info(`     score: ${c.score.toFixed(2)} = [${c.reasons.join(' × ')}]`);
     });
   }
 
diff --git a/gitnexus/src/core/ingestion/scope-extractor-bridge.ts b/gitnexus/src/core/ingestion/scope-extractor-bridge.ts
index fc63f29bf..41a50193d 100644
--- a/gitnexus/src/core/ingestion/scope-extractor-bridge.ts
+++ b/gitnexus/src/core/ingestion/scope-extractor-bridge.ts
@@ -28,6 +28,7 @@ import type { ParsedFile } from 'gitnexus-shared';
 import { extract as extractScope } from './scope-extractor.js';
 import type { LanguageProvider } from './language-provider.js';
 
+import { logger } from '../logger.js';
 /** Callback used to report scope-extraction warnings to the host (worker or direct). */
 export type ScopeBridgeWarn = (message: string) => void;
 
@@ -53,8 +54,7 @@ export function extractParsedFile(
       err instanceof Error ? err.message : String(err)
     }`;
     if (onWarn !== undefined) onWarn(message);
-    // eslint-disable-next-line no-console -- TODO(pino-migration)
-    else console.warn(message);
+    logger.warn(message);
     return undefined;
   }
 }
diff --git a/gitnexus/src/core/ingestion/scope-resolution/pipeline/phase.ts b/gitnexus/src/core/ingestion/scope-resolution/pipeline/phase.ts
index 900a7f1fd..c2fda9777 100644
--- a/gitnexus/src/core/ingestion/scope-resolution/pipeline/phase.ts
+++ b/gitnexus/src/core/ingestion/scope-resolution/pipeline/phase.ts
@@ -38,6 +38,7 @@ import { runScopeResolution } from './run.js';
 import { SCOPE_RESOLVERS } from './registry.js';
 import { isDev, isSemanticModelValidatorEnabled } from '../../utils/env.js';
 
+import { logger } from '../../../logger.js';
 export interface ScopeResolutionOutput {
   /** True when at least one language ran. */
   readonly ran: boolean;
@@ -144,8 +145,7 @@ export const scopeResolutionPhase: PipelinePhase<ScopeResolutionOutput> = {
           resolutionConfig,
           onWarn: (msg) => {
             if (isSemanticModelValidatorEnabled()) {
-              // eslint-disable-next-line no-console -- TODO(pino-migration)
-              console.warn(`[scope-resolution:${lang}] ${msg}`);
+              logger.warn(`[scope-resolution:${lang}] ${msg}`);
             }
           },
         },
@@ -163,8 +163,7 @@ export const scopeResolutionPhase: PipelinePhase<ScopeResolutionOutput> = {
       });
 
       if (isDev) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.log(
+        logger.info(
           `[scope-resolution:${lang}] ${stats.filesProcessed} files → ${stats.importsEmitted} IMPORTS + ${stats.referenceEdgesEmitted} reference edges (${stats.resolve.unresolved} unresolved sites, ${stats.referenceSkipped} skipped)`,
         );
       }
diff --git a/gitnexus/src/core/ingestion/scope-resolution/pipeline/run.ts b/gitnexus/src/core/ingestion/scope-resolution/pipeline/run.ts
index 947db5eb7..558c9ef30 100644
--- a/gitnexus/src/core/ingestion/scope-resolution/pipeline/run.ts
+++ b/gitnexus/src/core/ingestion/scope-resolution/pipeline/run.ts
@@ -41,6 +41,7 @@ import { emitImportEdges } from '../graph-bridge/imports-to-edges.js';
 import type { ScopeResolver } from '../contract/scope-resolver.js';
 import { buildWorkspaceResolutionIndex } from '../workspace-index.js';
 
+import { logger } from '../../../logger.js';
 interface RunScopeResolutionInput {
   readonly graph: KnowledgeGraph;
   /**
@@ -279,8 +280,7 @@ export function runScopeResolution(
   if (PROF) {
     const tEnd = process.hrtime.bigint();
     const ns = (a: bigint, b: bigint): number => Number(b - a) / 1_000_000;
-    // eslint-disable-next-line no-console -- TODO(pino-migration)
-    console.warn(
+    logger.warn(
       `[scope-resolution prof] extract=${ns(tStart, tExtract).toFixed(0)}ms` +
         ` finalize=${ns(tExtract, tFinalize).toFixed(0)}ms` +
         ` propagate=${ns(tFinalize, tPropagate).toFixed(0)}ms` +
diff --git a/gitnexus/src/core/ingestion/type-env.ts b/gitnexus/src/core/ingestion/type-env.ts
index 011655f5f..a38df617b 100644
--- a/gitnexus/src/core/ingestion/type-env.ts
+++ b/gitnexus/src/core/ingestion/type-env.ts
@@ -24,6 +24,7 @@ import {
 import type { SemanticModel } from './model/index.js';
 import type { NodeLabel } from 'gitnexus-shared';
 
+import { logger } from '../logger.js';
 /**
  * Per-file scoped type environment: maps (scope, variableName) → typeName.
  * Scope-aware: variables inside functions are keyed by function name,
@@ -769,8 +770,7 @@ const resolveFixpointBindings = (
     if (iter === MAX_FIXPOINT_ITERATIONS - 1 && process.env.GITNEXUS_DEBUG) {
       const unresolved = pendingItems.length - resolved.size;
       if (unresolved > 0) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.warn(
+        logger.warn(
           `[type-env] fixpoint hit iteration cap (${MAX_FIXPOINT_ITERATIONS}), ${unresolved} items unresolved`,
         );
       }
diff --git a/gitnexus/src/core/ingestion/utils/max-file-size.ts b/gitnexus/src/core/ingestion/utils/max-file-size.ts
index 8363ec946..82013783a 100644
--- a/gitnexus/src/core/ingestion/utils/max-file-size.ts
+++ b/gitnexus/src/core/ingestion/utils/max-file-size.ts
@@ -1,5 +1,6 @@
 import { TREE_SITTER_MAX_BUFFER } from '../constants.js';
 
+import { logger } from '../../logger.js';
 /** Default threshold (512 KB). Files larger than this are skipped by the walker. */
 export const DEFAULT_MAX_FILE_SIZE_BYTES = 512 * 1024;
 
@@ -11,8 +12,7 @@ const warned = new Set<string>();
 const warnOnce = (key: string, message: string): void => {
   if (warned.has(key)) return;
   warned.add(key);
-  // eslint-disable-next-line no-console -- TODO(pino-migration)
-  console.warn(message);
+  logger.warn(message);
 };
 
 /**
diff --git a/gitnexus/src/core/ingestion/workers/parse-worker.ts b/gitnexus/src/core/ingestion/workers/parse-worker.ts
index 80ba5e7b7..40734d858 100644
--- a/gitnexus/src/core/ingestion/workers/parse-worker.ts
+++ b/gitnexus/src/core/ingestion/workers/parse-worker.ts
@@ -85,6 +85,7 @@ import type { LanguageProvider } from '../language-provider.js';
 import type { ParsedFile } from 'gitnexus-shared';
 import { extractParsedFile } from '../scope-extractor-bridge.js';
 
+import { logger } from '../../logger.js';
 // ============================================================================
 // Types for serializable results
 // ============================================================================
@@ -1385,8 +1386,7 @@ const processFileGroup = (
     if (parentPort) {
       parentPort.postMessage({ type: 'warning', message });
     } else {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(message);
+      logger.warn(message);
     }
     return;
   }
@@ -1415,8 +1415,7 @@ const processFileGroup = (
         bufferSize: getTreeSitterBufferSize(parseContent),
       });
     } catch (err) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(
+      logger.warn(
         `Failed to parse file ${file.path}: ${err instanceof Error ? err.message : String(err)}`,
       );
       continue;
@@ -1429,8 +1428,7 @@ const processFileGroup = (
     try {
       matches = query.matches(tree.rootNode);
     } catch (err) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.warn(
+      logger.warn(
         `Query execution failed for ${file.path}: ${err instanceof Error ? err.message : String(err)}`,
       );
       continue;
@@ -1450,8 +1448,7 @@ const processFileGroup = (
       file.path,
       (message) => {
         if (parentPort) parentPort.postMessage({ type: 'warning', message });
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        else console.warn(message);
+        logger.warn(message);
       },
       tree,
     );
diff --git a/gitnexus/src/core/ingestion/workers/worker-pool.ts b/gitnexus/src/core/ingestion/workers/worker-pool.ts
index 5c02f2bd2..bcc9aa544 100644
--- a/gitnexus/src/core/ingestion/workers/worker-pool.ts
+++ b/gitnexus/src/core/ingestion/workers/worker-pool.ts
@@ -3,6 +3,7 @@ import os from 'node:os';
 import fs from 'node:fs';
 import { fileURLToPath } from 'node:url';
 
+import { logger } from '../../logger.js';
 export interface WorkerPool {
   /**
    * Dispatch items across workers. Items are split into bounded jobs, each job
@@ -258,8 +259,7 @@ export const createWorkerPool = (
             splitDepth: job.splitDepth + 1,
             timeoutMs: nextTimeout,
           };
-          // eslint-disable-next-line no-console -- TODO(pino-migration)
-          console.warn(
+          logger.warn(
             `Worker ${workerIndex} parse job idle timeout after ${job.timeoutMs / 1000}s ` +
               `(${job.items.length} items, ${job.estimatedBytes} bytes, last progress: ${lastProgress}). ` +
               `Splitting into ${first.items.length}/${second.items.length} item jobs with ` +
@@ -272,8 +272,7 @@ export const createWorkerPool = (
 
         const nextAttempt = job.attempt + 1;
         if (nextAttempt <= poolOptions.maxTimeoutRetries) {
-          // eslint-disable-next-line no-console -- TODO(pino-migration)
-          console.warn(
+          logger.warn(
             `Worker ${workerIndex} parse job idle timeout after ${job.timeoutMs / 1000}s ` +
               `(single item, attempt ${nextAttempt}/${poolOptions.maxTimeoutRetries + 1}). ` +
               `Retrying with ${nextTimeout / 1000}s timeout.`,
@@ -367,8 +366,7 @@ export const createWorkerPool = (
             reportProgress();
           } else if (msg.type === 'warning') {
             resetIdleTimer();
-            // eslint-disable-next-line no-console -- TODO(pino-migration)
-            console.warn(msg.message);
+            logger.warn(msg.message);
           } else if (msg.type === 'sub-batch-done') {
             waitingForFlush = true;
             resetIdleTimer();
diff --git a/gitnexus/src/core/lbug/extension-loader.ts b/gitnexus/src/core/lbug/extension-loader.ts
index 6ba78241b..582541942 100644
--- a/gitnexus/src/core/lbug/extension-loader.ts
+++ b/gitnexus/src/core/lbug/extension-loader.ts
@@ -1,6 +1,7 @@
 import { spawn } from 'child_process';
 import { fileURLToPath } from 'node:url';
 import { LBUG_MAX_DB_SIZE } from './lbug-config.js';
+import { logger } from '../logger.js';
 
 const DEFAULT_EXTENSION_INSTALL_TIMEOUT_MS = 15_000;
 const EXTENSION_NAME_PATTERN = /^[A-Za-z][A-Za-z0-9_]*$/;
@@ -188,8 +189,7 @@ export class ExtensionManager {
     const policy = opts.policy ?? this.options.policy ?? resolvePolicyFromEnv();
     const timeoutMs =
       opts.installTimeoutMs ?? this.options.installTimeoutMs ?? getExtensionInstallTimeoutMs();
-    // eslint-disable-next-line no-console -- TODO(pino-migration)
-    const warn = this.options.warn ?? console.warn;
+    const warn = this.options.warn ?? ((msg: string) => logger.warn(msg));
 
     if (policy === 'never') {
       this.markUnavailable(name, label, 'extension install policy is "never"', warn);
diff --git a/gitnexus/src/core/lbug/lbug-adapter.ts b/gitnexus/src/core/lbug/lbug-adapter.ts
index 61d856ce3..bbb8ef52c 100644
--- a/gitnexus/src/core/lbug/lbug-adapter.ts
+++ b/gitnexus/src/core/lbug/lbug-adapter.ts
@@ -24,6 +24,7 @@ import {
 } from './lbug-config.js';
 import { isVectorExtensionSupportedByPlatform } from '../platform/capabilities.js';
 
+import { logger } from '../logger.js';
 // ---------------------------------------------------------------------------
 // Relationship CSV splitting — extracted for testability (PR #818)
 // ---------------------------------------------------------------------------
@@ -348,8 +349,7 @@ const doInitLbug = async (dbPath: string) => {
     } catch (err) {
       const msg = err instanceof Error ? err.message : String(err);
       if (!msg.includes('already exists')) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.warn(`⚠️ Schema creation warning: ${msg.slice(0, 120)}`);
+        logger.warn(`⚠️ Schema creation warning: ${msg.slice(0, 120)}`);
       }
     }
   }
@@ -702,8 +702,7 @@ export const insertNodeToLbug = async (
     return false;
   } catch (e: any) {
     // Node may already exist or other error
-    // eslint-disable-next-line no-console -- TODO(pino-migration)
-    console.error(`Failed to insert ${label} node:`, e.message);
+    logger.error({ err: e.message }, `Failed to insert ${label} node:`);
     return false;
   }
 };
@@ -1030,16 +1029,14 @@ export const fetchExistingEmbeddingHashes = async (
           const nodeId = r.nodeId ?? r[0];
           if (nodeId) map.set(nodeId, STALE_HASH_SENTINEL);
         }
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.log(
+        logger.info(
           `[embed] ${map.size} nodes in legacy DB (missing chunk-aware columns) — all treated as stale`,
         );
         return map;
       } catch (fallbackErr: any) {
         const fallbackMsg = fallbackErr?.message ?? '';
         if (isMissingColumnOrTableError(fallbackMsg)) {
-          // eslint-disable-next-line no-console -- TODO(pino-migration)
-          console.log(
+          logger.info(
             `[embed] CodeEmbedding table not yet present — full embedding run (${fallbackMsg})`,
           );
           return undefined;
diff --git a/gitnexus/src/core/logger.ts b/gitnexus/src/core/logger.ts
index 3acbd0126..d97146a61 100644
--- a/gitnexus/src/core/logger.ts
+++ b/gitnexus/src/core/logger.ts
@@ -14,14 +14,23 @@
  *   const childLogger = createLogger('bridge-db', { debugEnvVar: 'GITNEXUS_DEBUG_BRIDGE' });
  *
  * Operator semantics:
- *   - Default level: 'warn'
+ *   - Default level: 'info' (matches pino default; preserves visibility of
+ *     existing `console.log` migrations)
  *   - When `opts.debugEnvVar` is set and that env var is truthy at
  *     createLogger time, that named child logs at level 'debug'
  *   - Output is NDJSON in production / CI / vitest. pino-pretty is used only
  *     when stdout is a TTY AND CI is unset AND VITEST is unset, so test
  *     and pipeline output stay parseable.
+ *
+ * Test capture:
+ *   The exported `logger` singleton is a Proxy that forwards every call to a
+ *   lazily-built pino instance. Tests use `_captureLogger()` to redirect that
+ *   inner instance to a memory stream so they can assert on records the
+ *   production code logged. See `gitnexus/test/unit/logger.test.ts` for the
+ *   pattern.
  */
 import pino, { type Logger, type LoggerOptions, type DestinationStream } from 'pino';
+import { Writable } from 'node:stream';
 
 export interface CreateLoggerOptions {
   /** When set, this env var (truthy at construction time) bumps level to 'debug'. */
@@ -37,19 +46,26 @@ function isTruthyEnv(value: string | undefined): boolean {
 }
 
 function shouldUsePretty(): boolean {
+  // Logger writes to stderr (fd 2) so CLI data on stdout (fd 1) stays clean.
+  // Pretty-print only when stderr is a TTY and not in CI/test environments.
   return (
-    process.stdout.isTTY === true && !isTruthyEnv(process.env.CI) && !isTruthyEnv(process.env.VITEST)
+    process.stderr.isTTY === true &&
+    !isTruthyEnv(process.env.CI) &&
+    !isTruthyEnv(process.env.VITEST)
   );
 }
 
 /**
- * Try to load pino-pretty synchronously via require(); fall back to raw NDJSON
- * if it isn't installed (production install with devDependencies pruned).
+ * Default pino destination — writes to stderr (fd 2) so CLI commands can
+ * keep stdout (fd 1) clean for tool data output (#324). Pino defaults to
+ * stdout; we override here.
  */
+function defaultDestination(): DestinationStream {
+  return pino.destination({ dest: 2, sync: true });
+}
+
 function tryBuildPrettyTransport(): LoggerOptions['transport'] | undefined {
   try {
-    // pino-pretty must be resolvable; if so, configure it as a transport target.
-    // pino's worker thread loads it by name at runtime.
     return {
       target: 'pino-pretty',
       options: {
@@ -65,8 +81,8 @@ function tryBuildPrettyTransport(): LoggerOptions['transport'] | undefined {
 
 function buildBaseOptions(): LoggerOptions {
   const opts: LoggerOptions = {
-    level: 'warn',
-    base: undefined, // omit pid/hostname from each record
+    level: 'info',
+    base: undefined,
   };
   if (shouldUsePretty()) {
     const transport = tryBuildPrettyTransport();
@@ -81,24 +97,101 @@ function buildBaseOptions(): LoggerOptions {
  * set and truthy at call time, the child runs at 'debug' level.
  */
 export function createLogger(name: string, opts?: CreateLoggerOptions): Logger {
-  const debugRequested = opts?.debugEnvVar
-    ? isTruthyEnv(process.env[opts.debugEnvVar])
-    : false;
+  const debugRequested = opts?.debugEnvVar ? isTruthyEnv(process.env[opts.debugEnvVar]) : false;
 
-  // When a custom destination is provided we cannot also use a transport
-  // (transports manage their own destination). Test path: just plain pino +
-  // destination stream.
   if (opts?.destination) {
     return pino(
-      { level: debugRequested ? 'debug' : 'warn', base: undefined, name },
+      { level: debugRequested ? 'debug' : 'info', base: undefined, name },
       opts.destination,
     );
   }
 
   const base = buildBaseOptions();
-  const root = pino({ ...base, level: debugRequested ? 'debug' : base.level });
+  // When using a transport (pino-pretty), pino manages the destination
+  // internally and we cannot pass one explicitly. When transport is absent,
+  // route to stderr so stdout stays clean for CLI data output.
+  const root = base.transport
+    ? pino({ ...base, level: debugRequested ? 'debug' : base.level })
+    : pino({ ...base, level: debugRequested ? 'debug' : base.level }, defaultDestination());
   return root.child({ name });
 }
 
-/** Default singleton logger; module name "gitnexus". */
-export const logger: Logger = createLogger('gitnexus');
+/* ------------------------------------------------------------------ */
+/*  Default singleton (Proxy-backed for test capture)                  */
+/* ------------------------------------------------------------------ */
+
+let _activeDestination: DestinationStream | undefined;
+let _cached: Logger | undefined;
+
+function _getInner(): Logger {
+  if (_cached) return _cached;
+  if (_activeDestination) {
+    _cached = pino({ level: 'info', base: undefined, name: 'gitnexus' }, _activeDestination);
+  } else {
+    // Use createLogger so the singleton honors the same stderr-by-default
+    // routing as named child loggers (CLI data on stdout stays clean).
+    _cached = createLogger('gitnexus');
+  }
+  return _cached;
+}
+
+/**
+ * Default singleton logger (`name: 'gitnexus'`). Backed by a Proxy so test
+ * capture (`_captureLogger()`) can redirect output without breaking modules
+ * that already imported the singleton at module-load time.
+ */
+export const logger = new Proxy({} as Logger, {
+  get(_target, prop) {
+    const inner = _getInner();
+    const value = (inner as unknown as Record<string | symbol, unknown>)[prop as string];
+    if (typeof value === 'function') {
+      return (value as (...a: unknown[]) => unknown).bind(inner);
+    }
+    return value;
+  },
+}) as Logger;
+
+/**
+ * Test helper. Redirects the default `logger` singleton to an in-memory
+ * stream and returns a capture object plus a restore function.
+ *
+ * Pattern:
+ *   let cap: ReturnType<typeof _captureLogger>;
+ *   beforeEach(() => { cap = _captureLogger(); });
+ *   afterEach(() => { cap.restore(); });
+ *   it('warns', () => {
+ *     fnUnderTest();
+ *     expect(cap.records().some(r => r.msg?.includes('clamping'))).toBe(true);
+ *   });
+ *
+ * Not a public API; underscore-prefixed and called only from test code.
+ */
+export function _captureLogger(): {
+  records(): Array<Record<string, unknown>>;
+  text(): string;
+  restore(): void;
+} {
+  class MemoryWritable extends Writable {
+    chunks: string[] = [];
+    _write(chunk: Buffer | string, _enc: BufferEncoding, cb: (err?: Error | null) => void): void {
+      this.chunks.push(typeof chunk === 'string' ? chunk : chunk.toString('utf-8'));
+      cb();
+    }
+  }
+  const w = new MemoryWritable();
+  _activeDestination = w;
+  _cached = undefined;
+  return {
+    records: () =>
+      w.chunks
+        .join('')
+        .split('\n')
+        .filter((l) => l.length > 0)
+        .map((l) => JSON.parse(l) as Record<string, unknown>),
+    text: () => w.chunks.join(''),
+    restore: () => {
+      _activeDestination = undefined;
+      _cached = undefined;
+    },
+  };
+}
diff --git a/gitnexus/src/core/tree-sitter/parser-loader.ts b/gitnexus/src/core/tree-sitter/parser-loader.ts
index f5e65c5e1..1312dabf3 100644
--- a/gitnexus/src/core/tree-sitter/parser-loader.ts
+++ b/gitnexus/src/core/tree-sitter/parser-loader.ts
@@ -2,6 +2,7 @@ import Parser from 'tree-sitter';
 import { createRequire } from 'node:module';
 import { SupportedLanguages } from 'gitnexus-shared';
 
+import { logger } from '../logger.js';
 const _require = createRequire(import.meta.url);
 
 /**
@@ -175,10 +176,8 @@ const logFailure = (key: string, result: LoadResult): void => {
   logged.add(key);
   const message = `[gitnexus] ${result.note} (${result.error.message})`;
 
-  // eslint-disable-next-line no-console -- TODO(pino-migration)
-  if (result.severity === 'error') console.error(message);
-  // eslint-disable-next-line no-console -- TODO(pino-migration)
-  else console.warn(message);
+  logger.error(message);
+  logger.warn(message);
 };
 
 export const resolveLanguageKey = (language: SupportedLanguages, filePath?: string): string =>
diff --git a/gitnexus/src/core/wiki/cursor-client.ts b/gitnexus/src/core/wiki/cursor-client.ts
index e0b85463c..bf85f4183 100644
--- a/gitnexus/src/core/wiki/cursor-client.ts
+++ b/gitnexus/src/core/wiki/cursor-client.ts
@@ -10,6 +10,7 @@
 import { spawn, execSync } from 'child_process';
 import type { LLMResponse, CallLLMOptions } from './llm-client.js';
 
+import { logger } from '../logger.js';
 export interface CursorConfig {
   model?: string;
   workingDirectory?: string;
@@ -21,8 +22,7 @@ function isVerbose(): boolean {
 
 function verboseLog(...args: unknown[]): void {
   if (isVerbose()) {
-    // eslint-disable-next-line no-console -- TODO(pino-migration)
-    console.log('[cursor-cli]', ...args);
+    logger.info({ args }, '[cursor-cli]');
   }
 }
 
diff --git a/gitnexus/src/core/wiki/llm-client.ts b/gitnexus/src/core/wiki/llm-client.ts
index 1a69453e5..f68c2d3e7 100644
--- a/gitnexus/src/core/wiki/llm-client.ts
+++ b/gitnexus/src/core/wiki/llm-client.ts
@@ -1,3 +1,4 @@
+import { logger } from '../logger.js';
 /**
  * LLM Client for Wiki Generation
  *
@@ -135,8 +136,7 @@ export async function callLLM(
 
   // Warn when using Azure legacy deployment URL without api-version
   if (azure && !config.apiVersion && config.baseUrl.includes('/deployments/')) {
-    // eslint-disable-next-line no-console -- TODO(pino-migration)
-    console.warn(
+    logger.warn(
       '[gitnexus] Warning: Azure legacy deployment URL detected but no api-version set. Add --api-version 2024-10-21 or use the v1 API format.',
     );
   }
diff --git a/gitnexus/src/mcp/core/embedder.ts b/gitnexus/src/mcp/core/embedder.ts
index 241d8ee06..336c565b8 100644
--- a/gitnexus/src/mcp/core/embedder.ts
+++ b/gitnexus/src/mcp/core/embedder.ts
@@ -15,6 +15,7 @@ import { resolveEmbeddingConfig } from '../../core/embeddings/config.js';
 import { applyHfEnvOverrides } from '../../core/embeddings/hf-env.js';
 import { silenceStdout, restoreStdout, realStderrWrite } from '../../core/lbug/pool-adapter.js';
 
+import { logger } from '../../core/logger.js';
 // Model config
 const MODEL_ID = 'Snowflake/snowflake-arctic-embed-xs';
 
@@ -51,8 +52,7 @@ export const initEmbedder = async (): Promise<FeatureExtractionPipeline> => {
       applyHfEnvOverrides(env);
       const embeddingConfig = resolveEmbeddingConfig();
 
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.error('GitNexus: Loading embedding model (first search may take a moment)...');
+      logger.error('GitNexus: Loading embedding model (first search may take a moment)...');
 
       const devicesToTry: Array<'dml' | 'cuda' | 'cpu'> =
         embeddingConfig.device === 'dml' || embeddingConfig.device === 'cuda'
@@ -83,8 +83,7 @@ export const initEmbedder = async (): Promise<FeatureExtractionPipeline> => {
             restoreStdout();
             process.stderr.write = realStderrWrite;
           }
-          // eslint-disable-next-line no-console -- TODO(pino-migration)
-          console.error(`GitNexus: Embedding model loaded (${device})`);
+          logger.error(`GitNexus: Embedding model loaded (${device})`);
           return embedderInstance!;
         } catch {
           if (device === 'cpu') throw new Error('Failed to load embedding model');
diff --git a/gitnexus/src/mcp/local/local-backend.ts b/gitnexus/src/mcp/local/local-backend.ts
index d8fba7af0..fade093ea 100644
--- a/gitnexus/src/mcp/local/local-backend.ts
+++ b/gitnexus/src/mcp/local/local-backend.ts
@@ -41,6 +41,7 @@ import {
 } from '../../core/platform/capabilities.js';
 import { PhaseTimer } from '../../core/search/phase-timer.js';
 import { checkStaleness, checkCwdMatch } from '../../core/git-staleness.js';
+import { logger } from '../../core/logger.js';
 // AI context generation is CLI-only (gitnexus analyze)
 // import { generateAIContextFiles } from '../../cli/ai-context.js';
 
@@ -164,8 +165,7 @@ const confidenceForRelType = (relType: string | undefined): number =>
 /** Structured error logging for query failures — replaces empty catch blocks */
 function logQueryError(context: string, err: unknown): void {
   const msg = err instanceof Error ? err.message : String(err);
-  // eslint-disable-next-line no-console -- TODO(pino-migration)
-  console.error(`GitNexus [${context}]: ${msg}`);
+  logger.error(`GitNexus [${context}]: ${msg}`);
 }
 
 /**
@@ -185,8 +185,7 @@ function logQueryError(context: string, err: unknown): void {
 function logQueryTiming(query: string, phases: Record<string, number>): void {
   const totalMs = phases.wall ?? Object.values(phases).reduce((a, b) => a + b, 0);
   const truncated = query.length > 80 ? `${query.slice(0, 80)}…` : query;
-  // eslint-disable-next-line no-console -- TODO(pino-migration)
-  console.error(
+  logger.error(
     `GitNexus [query:timing] query=${JSON.stringify(truncated)} totalMs=${totalMs} phases=${JSON.stringify(phases)}`,
   );
 }
@@ -289,8 +288,7 @@ export class LocalBackend {
       // If kuzu exists but lbug doesn't, warn so the user knows to re-analyze.
       const kuzu = await cleanupOldKuzuFiles(storagePath);
       if (kuzu.found && kuzu.needsReindex) {
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.error(
+        logger.error(
           `GitNexus: "${entry.name}" has a stale KuzuDB index. Run: gitnexus analyze ${entry.path}`,
         );
       }
@@ -640,8 +638,7 @@ export class LocalBackend {
     }
 
     this.warnedSiblingDrift.add(cacheKey);
-    // eslint-disable-next-line no-console -- TODO(pino-migration)
-    console.error(`GitNexus: ${match.hint}`);
+    logger.error(`GitNexus: ${match.hint}`);
   }
 
   // ─── Tool Dispatch ───────────────────────────────────────────────
@@ -994,8 +991,10 @@ export class LocalBackend {
     try {
       bm25Results = await searchFTSFromLbug(query, limit, repo.id);
     } catch (err: any) {
-      // eslint-disable-next-line no-console -- TODO(pino-migration)
-      console.error('GitNexus: BM25/FTS search failed (FTS indexes may not exist) -', err.message);
+      logger.error(
+        { err: err.message },
+        'GitNexus: BM25/FTS search failed (FTS indexes may not exist) -',
+      );
       return { results: [], ftsUsed: false };
     }
 
@@ -1119,8 +1118,7 @@ export class LocalBackend {
         // policy. Emitted once per `LocalBackend` instance lifetime to avoid
         // noisy stderr on hot semantic-search paths (DoD §2.8).
         this.warnedVectorUnsupported = true;
-        // eslint-disable-next-line no-console -- TODO(pino-migration)
-        console.error(
+        logger.error(
           'GitNexus [query:vector]: VECTOR extension not supported on this platform; using exact scan fallback',
         );
       }
diff --git a/gitnexus/test/integration/filesystem-walker.test.ts b/gitnexus/test/integration/filesystem-walker.test.ts
index accb24e37..2a1257ccc 100644
--- a/gitnexus/test/integration/filesystem-walker.test.ts
+++ b/gitnexus/test/integration/filesystem-walker.test.ts
@@ -8,6 +8,7 @@ import {
 } from '../../src/core/ingestion/filesystem-walker.js';
 import { _resetMaxFileSizeWarnings } from '../../src/core/ingestion/utils/max-file-size.js';
 
+import { _captureLogger } from '../../src/core/logger.js';
 describe('filesystem-walker', () => {
   let tmpDir: string;
 
@@ -328,7 +329,7 @@ describe('filesystem-walker', () => {
     const BIG_FILE = 'src/big.ts';
     const BIG_FILE_BYTES = 600 * 1024;
     const ORIGINAL_ENV = process.env.GITNEXUS_MAX_FILE_SIZE;
-    let warnSpy: ReturnType<typeof vi.spyOn>;
+    let cap: ReturnType<typeof _captureLogger>;
 
     beforeAll(async () => {
       sizeDir = await fs.mkdtemp(path.join(os.tmpdir(), 'gn-walker-size-test-'));
@@ -344,7 +345,7 @@ describe('filesystem-walker', () => {
     beforeEach(() => {
       delete process.env.GITNEXUS_MAX_FILE_SIZE;
       _resetMaxFileSizeWarnings();
-      warnSpy = vi.spyOn(console, 'warn').mockImplementation(() => undefined);
+      cap = _captureLogger();
     });
 
     afterEach(() => {
@@ -353,7 +354,7 @@ describe('filesystem-walker', () => {
       } else {
         process.env.GITNEXUS_MAX_FILE_SIZE = ORIGINAL_ENV;
       }
-      warnSpy.mockRestore();
+      cap.restore();
     });
 
     it('skips a 600KB file by default', async () => {
@@ -375,27 +376,27 @@ describe('filesystem-walker', () => {
       const files = await walkRepositoryPaths(sizeDir);
       const paths = files.map((f) => f.path.replace(/\\/g, '/'));
       expect(paths).not.toContain(BIG_FILE);
-      const invalidWarnings = warnSpy.mock.calls.filter((c) =>
-        String(c[0]).includes('must be a positive integer'),
-      );
+      const invalidWarnings = cap
+        .records()
+        .filter((r) => String(r.msg ?? '').includes('must be a positive integer'));
       expect(invalidWarnings).toHaveLength(1);
     });
 
     it('omits the "generated/vendored" suffix when threshold is overridden', async () => {
       process.env.GITNEXUS_MAX_FILE_SIZE = '1';
       await walkRepositoryPaths(sizeDir);
-      const skipWarnings = warnSpy.mock.calls.filter((c) => String(c[0]).includes('Skipped '));
+      const skipWarnings = cap.records().filter((r) => String(r.msg ?? '').includes('Skipped '));
       expect(skipWarnings.length).toBeGreaterThan(0);
-      for (const call of skipWarnings) {
-        expect(String(call[0])).not.toContain('generated/vendored');
+      for (const r of skipWarnings) {
+        expect(String(r.msg ?? '')).not.toContain('generated/vendored');
       }
     });
 
     it('keeps the "generated/vendored" suffix under the default threshold', async () => {
       await walkRepositoryPaths(sizeDir);
-      const skipWarnings = warnSpy.mock.calls.filter((c) => String(c[0]).includes('Skipped '));
+      const skipWarnings = cap.records().filter((r) => String(r.msg ?? '').includes('Skipped '));
       expect(skipWarnings.length).toBeGreaterThan(0);
-      expect(String(skipWarnings[0][0])).toContain('generated/vendored');
+      expect(String(skipWarnings[0].msg ?? '')).toContain('generated/vendored');
     });
   });
 });
diff --git a/gitnexus/test/integration/worker-pool.test.ts b/gitnexus/test/integration/worker-pool.test.ts
index eb0baebdf..f53375db0 100644
--- a/gitnexus/test/integration/worker-pool.test.ts
+++ b/gitnexus/test/integration/worker-pool.test.ts
@@ -13,6 +13,7 @@ import path from 'node:path';
 import fs from 'node:fs';
 import os from 'node:os';
 
+import { _captureLogger } from '../../src/core/logger.js';
 const DIST_WORKER = path.resolve(
   __dirname,
   '..',
@@ -211,7 +212,7 @@ describe('worker pool integration', () => {
     `,
     );
 
-    const warnSpy = vi.spyOn(console, 'warn').mockImplementation(() => undefined);
+    const cap = _captureLogger();
     const workerUrl = pathToFileURL(workerPath) as URL;
     pool = createWorkerPool(workerUrl, 1);
 
@@ -221,9 +222,9 @@ describe('worker pool integration', () => {
       ]);
       expect(results).toHaveLength(1);
       expect(results[0].fileCount).toBe(1);
-      expect(warnSpy).toHaveBeenCalledWith('warning before result');
+      expect(cap.records().some((r) => r.msg === 'warning before result')).toBe(true);
     } finally {
-      warnSpy.mockRestore();
+      cap.restore();
       fs.rmSync(tempDir, { recursive: true, force: true });
     }
   });
@@ -298,7 +299,7 @@ describe('worker pool integration', () => {
     `,
     );
 
-    const warnSpy = vi.spyOn(console, 'warn').mockImplementation(() => undefined);
+    const cap = _captureLogger();
     pool = createWorkerPool(pathToFileURL(workerPath) as URL, 1, {
       subBatchIdleTimeoutMs: 150,
       maxTimeoutRetries: 1,
@@ -308,9 +309,11 @@ describe('worker pool integration', () => {
     try {
       const results = await pool.dispatch<any, any>([{ path: 'retry.ts', content: '' }]);
       expect(results).toEqual([{ fileCount: 1, recovered: true }]);
-      expect(warnSpy).toHaveBeenCalledWith(expect.stringContaining('Retrying with 0.6s timeout'));
+      expect(
+        cap.records().some((r) => String(r.msg ?? '').includes('Retrying with 0.6s timeout')),
+      ).toBe(true);
     } finally {
-      warnSpy.mockRestore();
+      cap.restore();
       fs.rmSync(tempDir, { recursive: true, force: true });
     }
   });
@@ -344,7 +347,7 @@ describe('worker pool integration', () => {
     `,
     );
 
-    const warnSpy = vi.spyOn(console, 'warn').mockImplementation(() => undefined);
+    const cap = _captureLogger();
     pool = createWorkerPool(pathToFileURL(workerPath) as URL, 1, {
       subBatchSize: 2,
       subBatchIdleTimeoutMs: 150,
@@ -372,9 +375,11 @@ describe('worker pool integration', () => {
       ]);
       expect(progressCalls).toEqual([...progressCalls].sort((a, b) => a - b));
       expect(progressCalls.at(-1)).toBe(4);
-      expect(warnSpy).toHaveBeenCalledWith(expect.stringContaining('Splitting into 1/1 item jobs'));
+      expect(
+        cap.records().some((r) => String(r.msg ?? '').includes('Splitting into 1/1 item jobs')),
+      ).toBe(true);
     } finally {
-      warnSpy.mockRestore();
+      cap.restore();
       fs.rmSync(tempDir, { recursive: true, force: true });
     }
   });
@@ -440,7 +445,7 @@ describe('worker pool integration', () => {
     `,
     );
 
-    const warnSpy = vi.spyOn(console, 'warn').mockImplementation(() => undefined);
+    const cap = _captureLogger();
     pool = createWorkerPool(pathToFileURL(workerPath) as URL, 2, {
       subBatchSize: 2,
       subBatchIdleTimeoutMs: 150,
@@ -466,9 +471,11 @@ describe('worker pool integration', () => {
         'tail-a.ts',
         'tail-b.ts',
       ]);
-      expect(warnSpy).toHaveBeenCalledWith(expect.stringContaining('Splitting into 1/1 item jobs'));
+      expect(
+        cap.records().some((r) => String(r.msg ?? '').includes('Splitting into 1/1 item jobs')),
+      ).toBe(true);
     } finally {
-      warnSpy.mockRestore();
+      cap.restore();
       fs.rmSync(tempDir, { recursive: true, force: true });
     }
   });
@@ -504,7 +511,7 @@ describe('worker pool integration', () => {
     `,
     );
 
-    const warnSpy = vi.spyOn(console, 'warn').mockImplementation(() => undefined);
+    const cap = _captureLogger();
     // 2 workers but subBatchSize=4 means all 4 items form 1 job; second worker stays idle.
     pool = createWorkerPool(pathToFileURL(workerPath) as URL, 2, {
       subBatchSize: 4,
@@ -523,9 +530,9 @@ describe('worker pool integration', () => {
 
       const allPaths = results.flatMap((r: any) => r.paths);
       expect(allPaths.sort()).toEqual(['a.ts', 'b.ts', 'c.ts', 'd.ts']);
-      expect(warnSpy).toHaveBeenCalledWith(expect.stringContaining('Splitting into'));
+      expect(cap.records().some((r) => String(r.msg ?? '').includes('Splitting into'))).toBe(true);
     } finally {
-      warnSpy.mockRestore();
+      cap.restore();
       fs.rmSync(tempDir, { recursive: true, force: true });
     }
   }, 15_000);
diff --git a/gitnexus/test/unit/analyze-worker-timeout.test.ts b/gitnexus/test/unit/analyze-worker-timeout.test.ts
index dcf5a9dce..e23c0a906 100644
--- a/gitnexus/test/unit/analyze-worker-timeout.test.ts
+++ b/gitnexus/test/unit/analyze-worker-timeout.test.ts
@@ -39,6 +39,8 @@ describe('analyzeCommand worker timeout validation', () => {
   it.each(['0', 'abc', '-5', 'Infinity'])(
     'rejects invalid --worker-timeout value %s before analysis starts',
     async (workerTimeout) => {
+      // CLI code (cli/analyze.ts) is exempt from the pino migration —
+      // user-facing stdout/stderr is the contract. Spy on console.error.
       const errorSpy = vi.spyOn(console, 'error').mockImplementation(() => undefined);
       const { analyzeCommand } = await import('../../src/cli/analyze.js');
 
diff --git a/gitnexus/test/unit/calltool-dispatch.test.ts b/gitnexus/test/unit/calltool-dispatch.test.ts
index aa422327b..f8d94d890 100644
--- a/gitnexus/test/unit/calltool-dispatch.test.ts
+++ b/gitnexus/test/unit/calltool-dispatch.test.ts
@@ -71,6 +71,7 @@ vi.mock('../../src/mcp/core/embedder.js', () => ({
 
 import { LocalBackend } from '../../src/mcp/local/local-backend.js';
 import { listRegisteredRepos, cleanupOldKuzuFiles } from '../../src/storage/repo-manager.js';
+import { _captureLogger } from '../../src/core/logger.js';
 import {
   initLbug,
   executeQuery,
@@ -194,7 +195,7 @@ describe('LocalBackend.callTool', () => {
   });
 
   it('skips vector index query when VECTOR is unsupported by the platform', async () => {
-    const consoleError = vi.spyOn(console, 'error').mockImplementation(() => undefined);
+    const cap = _captureLogger();
     platformMocks.isVectorExtensionSupportedByPlatform.mockReturnValue(false);
     (executeQuery as any).mockImplementation(async (_repoId: string, cypher: string) => {
       if (cypher.includes('COUNT(*) AS cnt')) return [{ cnt: 1 }];
@@ -217,13 +218,17 @@ describe('LocalBackend.callTool', () => {
             cypher.includes('e.embedding AS embedding'),
         ),
       ).toBe(true);
-      expect(consoleError).toHaveBeenCalledWith(
-        expect.stringContaining(
-          'GitNexus [query:vector]: VECTOR extension not supported on this platform',
-        ),
-      );
+      expect(
+        cap
+          .records()
+          .some((r) =>
+            String(r.msg ?? '').includes(
+              'GitNexus [query:vector]: VECTOR extension not supported on this platform',
+            ),
+          ),
+      ).toBe(true);
     } finally {
-      consoleError.mockRestore();
+      cap.restore();
     }
   });
 
@@ -835,7 +840,7 @@ describe('LocalBackend.resolveRepo', () => {
       hint: '⚠️ stale sibling clone',
     });
 
-    const errSpy = vi.spyOn(console, 'error').mockImplementation(() => {});
+    const cap = _captureLogger();
     try {
       await backend.init();
 
@@ -846,13 +851,15 @@ describe('LocalBackend.resolveRepo', () => {
       await backend.resolveRepo();
       await backend.resolveRepo();
 
-      const drift = errSpy.mock.calls.filter((c) => String(c[0]).includes('stale sibling clone'));
+      const drift = cap
+        .records()
+        .filter((r) => String(r.msg ?? '').includes('stale sibling clone'));
       expect(drift).toHaveLength(1);
       // checkCwdMatch should also only run once — the cache check
       // happens BEFORE the shellout-heavy match call.
       expect(checkCwdMatch).toHaveBeenCalledTimes(1);
     } finally {
-      errSpy.mockRestore();
+      cap.restore();
       (checkCwdMatch as any).mockResolvedValue({ match: 'none' });
     }
   });
diff --git a/gitnexus/test/unit/group/grpc-extractor.test.ts b/gitnexus/test/unit/group/grpc-extractor.test.ts
index a586b5c0d..fc05eac8e 100644
--- a/gitnexus/test/unit/group/grpc-extractor.test.ts
+++ b/gitnexus/test/unit/group/grpc-extractor.test.ts
@@ -11,6 +11,7 @@ import {
 } from '../../../src/core/group/extractors/grpc-extractor.js';
 import type { ProtoServiceInfo } from '../../../src/core/group/extractors/grpc-extractor.js';
 import type { RepoHandle } from '../../../src/core/group/types.js';
+import { _captureLogger } from '../../../src/core/logger.js';
 
 describe('GrpcExtractor', () => {
   let tmpDir: string;
@@ -581,6 +582,7 @@ service AuthService {
 import type { ClientGrpc } from '@nestjs/microservices';
 import { AuthServiceClient } from './generated/auth';
 
+import { _captureLogger } from '../../../src/core/logger.js';
 export class AuthGateway {
   constructor(private readonly client: ClientGrpc) {}
 
@@ -797,18 +799,18 @@ describe('resolveProtoConflict', () => {
   });
 
   it('test_all_zero_tie_returns_null', () => {
-    const warnSpy = vi.spyOn(console, 'warn').mockImplementation(() => {});
+    const cap = _captureLogger();
     const candidates = [
       makeInfo('pkgA', 'totally/unrelated/a/svc.proto'),
       makeInfo('pkgB', 'completely/different/b/svc.proto'),
     ];
     const result = resolveProtoConflict('Svc', 'src/main.go', candidates);
     expect(result).toBeNull();
-    warnSpy.mockRestore();
+    cap.restore();
   });
 
   it('test_positive_score_tie_returns_null', () => {
-    const warnSpy = vi.spyOn(console, 'warn').mockImplementation(() => {});
+    const cap = _captureLogger();
     // Both candidates share `src/proto` with the source dir — equal shared runs.
     const candidates = [
       makeInfo('pkgA', 'src/proto/a/svc.proto'),
@@ -816,11 +818,11 @@ describe('resolveProtoConflict', () => {
     ];
     const result = resolveProtoConflict('Svc', 'src/proto/main.go', candidates);
     expect(result).toBeNull();
-    warnSpy.mockRestore();
+    cap.restore();
   });
 
   it('test_three_way_zero_tie_returns_null', () => {
-    const warnSpy = vi.spyOn(console, 'warn').mockImplementation(() => {});
+    const cap = _captureLogger();
     const candidates = [
       makeInfo('pkgA', 'aaa/svc.proto'),
       makeInfo('pkgB', 'bbb/svc.proto'),
@@ -828,7 +830,7 @@ describe('resolveProtoConflict', () => {
     ];
     const result = resolveProtoConflict('Svc', 'src/main.go', candidates);
     expect(result).toBeNull();
-    warnSpy.mockRestore();
+    cap.restore();
   });
 
   it('test_unique_winner_among_ties', () => {
@@ -843,19 +845,19 @@ describe('resolveProtoConflict', () => {
   });
 
   it('test_ambiguous_emits_single_warn_with_service_and_paths', () => {
-    const warnSpy = vi.spyOn(console, 'warn').mockImplementation(() => {});
+    const cap = _captureLogger();
     const candidates = [
       makeInfo('pkgA', 'totally/unrelated/a/svc.proto'),
       makeInfo('pkgB', 'completely/different/b/svc.proto'),
     ];
     resolveProtoConflict('MyService', 'src/main.go', candidates);
-    expect(warnSpy).toHaveBeenCalledTimes(1);
-    const msg = String(warnSpy.mock.calls[0][0]);
+    expect(cap.records().length).toBe(1);
+    const msg = String(String(cap.records()[0]?.msg ?? ''));
     expect(msg).toContain('MyService');
     expect(msg).toContain('src/main.go');
     expect(msg).toContain('totally/unrelated/a/svc.proto');
     expect(msg).toContain('completely/different/b/svc.proto');
-    warnSpy.mockRestore();
+    cap.restore();
   });
 });
 
@@ -879,7 +881,7 @@ describe('GrpcExtractor.extract ambiguous proto resolution', () => {
   });
 
   it('test_ambiguous_short_name_across_unrelated_protos_yields_no_source_contract', async () => {
-    const warnSpy = vi.spyOn(console, 'warn').mockImplementation(() => {});
+    const cap = _captureLogger();
     // Two unrelated proto files defining the same short name `UserService` in
     // unrelated directories, neither sharing path segments with the Go source.
     await fsp.mkdir(path.join(tmpDir, 'billing-team', 'proto'), { recursive: true });
@@ -906,8 +908,8 @@ describe('GrpcExtractor.extract ambiguous proto resolution', () => {
       (c) => c.meta.source === 'go_client' && c.meta.service === 'UserService',
     );
     expect(sourceContracts).toHaveLength(0);
-    expect(warnSpy).toHaveBeenCalled();
-    warnSpy.mockRestore();
+    expect(cap.records().length).toBeGreaterThan(0);
+    cap.restore();
   });
 });
 
diff --git a/gitnexus/test/unit/group/rust-workspace-extractor.test.ts b/gitnexus/test/unit/group/rust-workspace-extractor.test.ts
index a9e277c36..3dd958ebf 100644
--- a/gitnexus/test/unit/group/rust-workspace-extractor.test.ts
+++ b/gitnexus/test/unit/group/rust-workspace-extractor.test.ts
@@ -3,6 +3,7 @@ import fs from 'node:fs/promises';
 import path from 'node:path';
 import os from 'node:os';
 import { extractRustWorkspaceLinks } from '../../../src/core/group/extractors/rust-workspace-extractor.js';
+import { _captureLogger } from '../../../src/core/logger.js';
 
 describe('RustWorkspaceExtractor', () => {
   let tmpDir: string;
@@ -229,19 +230,17 @@ describe('RustWorkspaceExtractor', () => {
       ['consumer', path.join(tmpDir, 'consumer')],
     ]);
 
-    const warnings: string[] = [];
-    const origWarn = console.warn;
-    console.warn = (...args: unknown[]) => {
-      warnings.push(String(args[0]));
-    };
+    const cap = _captureLogger();
     try {
       const result = await extractRustWorkspaceLinks(repos, repoPaths);
 
-      expect(warnings.some((w) => w.includes('duplicate crate name "shared"'))).toBe(true);
+      expect(
+        cap.records().some((r) => String(r.msg ?? '').includes('duplicate crate name "shared"')),
+      ).toBe(true);
       expect(result.links).toHaveLength(1);
       expect(result.links[0].from).toBe('a');
     } finally {
-      console.warn = origWarn;
+      cap.restore();
     }
   });
 
diff --git a/gitnexus/test/unit/group/sync.test.ts b/gitnexus/test/unit/group/sync.test.ts
index a6b6376c0..3cfc337a4 100644
--- a/gitnexus/test/unit/group/sync.test.ts
+++ b/gitnexus/test/unit/group/sync.test.ts
@@ -3,6 +3,7 @@ import * as fs from 'node:fs';
 import * as path from 'node:path';
 import * as os from 'node:os';
 import { syncGroup, stableRepoPoolId } from '../../../src/core/group/sync.js';
+import { _captureLogger } from '../../../src/core/logger.js';
 import type {
   GroupConfig,
   StoredContract,
@@ -292,9 +293,7 @@ describe('syncGroup', () => {
       matching: { bm25_threshold: 0.7, embedding_threshold: 0.65, max_candidates_per_step: 3 },
     };
 
-    const warnings: string[] = [];
-    const origWarn = console.warn;
-    console.warn = (msg: string) => warnings.push(String(msg));
+    const cap = _captureLogger();
     try {
       const result = await syncGroup(config, {
         extractorOverride: async () => [],
@@ -306,9 +305,9 @@ describe('syncGroup', () => {
       expect(result.crossLinks[0].to.symbolUid).toBe(
         'manifest::app/dangling::http::POST::/api/missing',
       );
-      expect(warnings.some((w) => w.includes('app/dangling'))).toBe(true);
+      expect(cap.records().some((r) => String(r.msg ?? '').includes('app/dangling'))).toBe(true);
     } finally {
-      console.warn = origWarn;
+      cap.restore();
     }
   });
 
diff --git a/gitnexus/test/unit/ignore-service.test.ts b/gitnexus/test/unit/ignore-service.test.ts
index de32eb8d9..05edf0e89 100644
--- a/gitnexus/test/unit/ignore-service.test.ts
+++ b/gitnexus/test/unit/ignore-service.test.ts
@@ -580,7 +580,7 @@ describe('loadIgnoreRules — error handling', () => {
       expect(result).toBeNull();
       expect(warnSpy).toHaveBeenCalledWith(expect.stringContaining('.gitignore'));
 
-      warnSpy.mockRestore();
+      cap.restore();
       await fs.chmod(gitignorePath, 0o644);
       await fs.unlink(gitignorePath);
     },
diff --git a/gitnexus/test/unit/logger.test.ts b/gitnexus/test/unit/logger.test.ts
index 32eadd3ed..b89b736a9 100644
--- a/gitnexus/test/unit/logger.test.ts
+++ b/gitnexus/test/unit/logger.test.ts
@@ -62,7 +62,7 @@ describe('createLogger — debugEnvVar gating', () => {
     delete process.env[ENV];
   });
 
-  it('without debugEnvVar, .debug() emits nothing (default warn level)', () => {
+  it('without debugEnvVar, .debug() emits nothing (default info level)', () => {
     const dest = new MemoryWritable();
     const log = createLogger('t', { destination: dest });
     log.debug('should not appear');
@@ -131,7 +131,12 @@ describe('createLogger — structured output safety', () => {
     // Exactly one record. The internal \r\n is JSON-escaped, not a record boundary.
     expect(dest.records().length).toBe(1);
     // Raw text has trailing newline as record terminator — count of \n == 1.
-    expect(dest.text().split('\n').filter((l) => l.length > 0).length).toBe(1);
+    expect(
+      dest
+        .text()
+        .split('\n')
+        .filter((l) => l.length > 0).length,
+    ).toBe(1);
   });
 
   it('U+2028 / U+2029 in a string field stays inside one NDJSON record', () => {
diff --git a/gitnexus/test/unit/max-file-size.test.ts b/gitnexus/test/unit/max-file-size.test.ts
index 074e148e7..569b41eab 100644
--- a/gitnexus/test/unit/max-file-size.test.ts
+++ b/gitnexus/test/unit/max-file-size.test.ts
@@ -1,4 +1,4 @@
-import { describe, it, expect, beforeEach, afterEach, vi } from 'vitest';
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
 import {
   DEFAULT_MAX_FILE_SIZE_BYTES,
   MAX_FILE_SIZE_UPPER_BOUND_BYTES,
@@ -6,15 +6,16 @@ import {
   getMaxFileSizeBannerMessage,
   _resetMaxFileSizeWarnings,
 } from '../../src/core/ingestion/utils/max-file-size.js';
+import { _captureLogger } from '../../src/core/logger.js';
 
 describe('getMaxFileSizeBytes', () => {
   const ORIGINAL = process.env.GITNEXUS_MAX_FILE_SIZE;
-  let warnSpy: ReturnType<typeof vi.spyOn>;
+  let cap: ReturnType<typeof _captureLogger>;
 
   beforeEach(() => {
     delete process.env.GITNEXUS_MAX_FILE_SIZE;
     _resetMaxFileSizeWarnings();
-    warnSpy = vi.spyOn(console, 'warn').mockImplementation(() => undefined);
+    cap = _captureLogger();
   });
 
   afterEach(() => {
@@ -23,43 +24,43 @@ describe('getMaxFileSizeBytes', () => {
     } else {
       process.env.GITNEXUS_MAX_FILE_SIZE = ORIGINAL;
     }
-    warnSpy.mockRestore();
+    cap.restore();
   });
 
   it('returns the default when the env var is unset', () => {
     expect(getMaxFileSizeBytes()).toBe(DEFAULT_MAX_FILE_SIZE_BYTES);
-    expect(warnSpy).not.toHaveBeenCalled();
+    expect(cap.records().length).toBe(0);
   });
 
   it('parses a positive integer value as KB', () => {
     process.env.GITNEXUS_MAX_FILE_SIZE = '1024';
     expect(getMaxFileSizeBytes()).toBe(1024 * 1024);
-    expect(warnSpy).not.toHaveBeenCalled();
+    expect(cap.records().length).toBe(0);
   });
 
   it('clamps values above the tree-sitter ceiling', () => {
-    // One KB above the 32 MB ceiling.
     const aboveCeilingKb = MAX_FILE_SIZE_UPPER_BOUND_BYTES / 1024 + 1;
     process.env.GITNEXUS_MAX_FILE_SIZE = String(aboveCeilingKb);
     expect(getMaxFileSizeBytes()).toBe(MAX_FILE_SIZE_UPPER_BOUND_BYTES);
-    expect(warnSpy).toHaveBeenCalledTimes(1);
-    expect(warnSpy.mock.calls[0][0]).toContain('clamping');
+    const records = cap.records();
+    expect(records.length).toBe(1);
+    expect(String(records[0].msg)).toContain('clamping');
   });
 
   it.each(['abc', '0', '-512', '1.5', 'NaN', ''])(
     'falls back to the default and warns on invalid value %s',
     (raw) => {
       if (raw === '') {
-        // Empty string is treated as unset by the util (raw falsy check).
         process.env.GITNEXUS_MAX_FILE_SIZE = raw;
         expect(getMaxFileSizeBytes()).toBe(DEFAULT_MAX_FILE_SIZE_BYTES);
-        expect(warnSpy).not.toHaveBeenCalled();
+        expect(cap.records().length).toBe(0);
         return;
       }
       process.env.GITNEXUS_MAX_FILE_SIZE = raw;
       expect(getMaxFileSizeBytes()).toBe(DEFAULT_MAX_FILE_SIZE_BYTES);
-      expect(warnSpy).toHaveBeenCalledTimes(1);
-      expect(warnSpy.mock.calls[0][0]).toContain('must be a positive integer');
+      const records = cap.records();
+      expect(records.length).toBe(1);
+      expect(String(records[0].msg)).toContain('must be a positive integer');
     },
   );
 
@@ -68,7 +69,7 @@ describe('getMaxFileSizeBytes', () => {
     getMaxFileSizeBytes();
     getMaxFileSizeBytes();
     getMaxFileSizeBytes();
-    expect(warnSpy).toHaveBeenCalledTimes(1);
+    expect(cap.records().length).toBe(1);
   });
 
   it('warns separately for distinct invalid values', () => {
@@ -76,20 +77,20 @@ describe('getMaxFileSizeBytes', () => {
     getMaxFileSizeBytes();
     process.env.GITNEXUS_MAX_FILE_SIZE = 'xyz';
     getMaxFileSizeBytes();
-    expect(warnSpy).toHaveBeenCalledTimes(2);
+    expect(cap.records().length).toBe(2);
   });
 
   it('_resetMaxFileSizeWarnings re-enables warnings after reset', () => {
     process.env.GITNEXUS_MAX_FILE_SIZE = 'abc';
     getMaxFileSizeBytes();
-    expect(warnSpy).toHaveBeenCalledTimes(1);
+    expect(cap.records().length).toBe(1);
 
     getMaxFileSizeBytes();
-    expect(warnSpy).toHaveBeenCalledTimes(1);
+    expect(cap.records().length).toBe(1);
 
     _resetMaxFileSizeWarnings();
     getMaxFileSizeBytes();
-    expect(warnSpy).toHaveBeenCalledTimes(2);
+    expect(cap.records().length).toBe(2);
   });
 
   it('DEFAULT_MAX_FILE_SIZE_BYTES is 512 KB', () => {
@@ -99,12 +100,12 @@ describe('getMaxFileSizeBytes', () => {
 
 describe('getMaxFileSizeBannerMessage', () => {
   const ORIGINAL = process.env.GITNEXUS_MAX_FILE_SIZE;
-  let warnSpy: ReturnType<typeof vi.spyOn>;
+  let cap: ReturnType<typeof _captureLogger>;
 
   beforeEach(() => {
     delete process.env.GITNEXUS_MAX_FILE_SIZE;
     _resetMaxFileSizeWarnings();
-    warnSpy = vi.spyOn(console, 'warn').mockImplementation(() => undefined);
+    cap = _captureLogger();
   });
 
   afterEach(() => {
@@ -113,7 +114,7 @@ describe('getMaxFileSizeBannerMessage', () => {
     } else {
       process.env.GITNEXUS_MAX_FILE_SIZE = ORIGINAL;
     }
-    warnSpy.mockRestore();
+    cap.restore();
   });
 
   it('returns null when the env var is unset (default threshold)', () => {
diff --git a/gitnexus/test/unit/sequential-language-availability.test.ts b/gitnexus/test/unit/sequential-language-availability.test.ts
index f48db5778..bd0e4d4d6 100644
--- a/gitnexus/test/unit/sequential-language-availability.test.ts
+++ b/gitnexus/test/unit/sequential-language-availability.test.ts
@@ -19,6 +19,7 @@ import { createSymbolTable } from '../../src/core/ingestion/model/symbol-table.j
 import { createResolutionContext } from '../../src/core/ingestion/model/resolution-context.js';
 import * as parserLoader from '../../src/core/tree-sitter/parser-loader.js';
 
+import { _captureLogger } from '../../src/core/logger.js';
 describe('sequential native parser availability', () => {
   beforeEach(() => {
     vi.clearAllMocks();
@@ -43,7 +44,7 @@ describe('sequential native parser availability', () => {
   });
 
   it('warns when processImports skips files in verbose mode', async () => {
-    const warnSpy = vi.spyOn(console, 'warn').mockImplementation(() => undefined);
+    const cap = _captureLogger();
     const previous = process.env.GITNEXUS_VERBOSE;
     process.env.GITNEXUS_VERBOSE = '1';
     vi.mocked(parserLoader.isLanguageAvailable).mockReturnValue(false);
@@ -58,11 +59,17 @@ describe('sequential native parser availability', () => {
       ['App.swift'],
     );
 
-    expect(warnSpy).toHaveBeenCalledWith(
-      '[ingestion] Skipped 1 swift file(s) in import processing — swift parser not available.',
-    );
+    expect(
+      cap
+        .records()
+        .some(
+          (r) =>
+            r.msg ===
+            '[ingestion] Skipped 1 swift file(s) in import processing — swift parser not available.',
+        ),
+    ).toBe(true);
 
-    warnSpy.mockRestore();
+    cap.restore();
     if (previous === undefined) {
       delete process.env.GITNEXUS_VERBOSE;
     } else {
@@ -86,7 +93,7 @@ describe('sequential native parser availability', () => {
   });
 
   it('warns when processCalls skips files in verbose mode', async () => {
-    const warnSpy = vi.spyOn(console, 'warn').mockImplementation(() => undefined);
+    const cap = _captureLogger();
     const previous = process.env.GITNEXUS_VERBOSE;
     process.env.GITNEXUS_VERBOSE = '1';
     vi.mocked(parserLoader.isLanguageAvailable).mockReturnValue(false);
@@ -98,11 +105,17 @@ describe('sequential native parser availability', () => {
       createResolutionContext(),
     );
 
-    expect(warnSpy).toHaveBeenCalledWith(
-      '[ingestion] Skipped 1 swift file(s) in call processing — swift parser not available.',
-    );
+    expect(
+      cap
+        .records()
+        .some(
+          (r) =>
+            r.msg ===
+            '[ingestion] Skipped 1 swift file(s) in call processing — swift parser not available.',
+        ),
+    ).toBe(true);
 
-    warnSpy.mockRestore();
+    cap.restore();
     if (previous === undefined) {
       delete process.env.GITNEXUS_VERBOSE;
     } else {
@@ -126,7 +139,7 @@ describe('sequential native parser availability', () => {
   });
 
   it('warns when processHeritage skips files in verbose mode', async () => {
-    const warnSpy = vi.spyOn(console, 'warn').mockImplementation(() => undefined);
+    const cap = _captureLogger();
     const previous = process.env.GITNEXUS_VERBOSE;
     process.env.GITNEXUS_VERBOSE = '1';
     vi.mocked(parserLoader.isLanguageAvailable).mockReturnValue(false);
@@ -138,11 +151,17 @@ describe('sequential native parser availability', () => {
       createResolutionContext(),
     );
 
-    expect(warnSpy).toHaveBeenCalledWith(
-      '[ingestion] Skipped 1 swift file(s) in heritage processing — swift parser not available.',
-    );
+    expect(
+      cap
+        .records()
+        .some(
+          (r) =>
+            r.msg ===
+            '[ingestion] Skipped 1 swift file(s) in heritage processing — swift parser not available.',
+        ),
+    ).toBe(true);
 
-    warnSpy.mockRestore();
+    cap.restore();
     if (previous === undefined) {
       delete process.env.GITNEXUS_VERBOSE;
     } else {
@@ -166,7 +185,7 @@ describe('sequential native parser availability', () => {
   });
 
   it('warns when processParsing skips files in verbose mode', async () => {
-    const warnSpy = vi.spyOn(console, 'warn').mockImplementation(() => undefined);
+    const cap = _captureLogger();
     const previous = process.env.GITNEXUS_VERBOSE;
     process.env.GITNEXUS_VERBOSE = '1';
     vi.mocked(parserLoader.isLanguageAvailable).mockReturnValue(false);
@@ -178,11 +197,17 @@ describe('sequential native parser availability', () => {
       createASTCache(),
     );
 
-    expect(warnSpy).toHaveBeenCalledWith(
-      '[ingestion] Skipped 1 swift file(s) in parsing processing — swift parser not available.',
-    );
+    expect(
+      cap
+        .records()
+        .some(
+          (r) =>
+            r.msg ===
+            '[ingestion] Skipped 1 swift file(s) in parsing processing — swift parser not available.',
+        ),
+    ).toBe(true);
 
-    warnSpy.mockRestore();
+    cap.restore();
     if (previous === undefined) {
       delete process.env.GITNEXUS_VERBOSE;
     } else {