diff --git a/CLAUDE.md b/CLAUDE.md
index d54ad954b..6d441c782 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -150,6 +150,8 @@ JS source is plain JavaScript (ES modules) in `src/`. No transpilation step. The
 - **MCP single-repo isolation:** `startMCPServer` defaults to single-repo mode — tools have no `repo` property and `list_repos` is not exposed. Passing `--multi-repo` or `--repos` to the CLI (or `options.multiRepo` / `options.allowedRepos` programmatically) enables multi-repo access. `buildToolList(multiRepo)` builds the tool list dynamically; the backward-compatible `TOOLS` export equals `buildToolList(true)`
 - **Credential resolution:** `loadConfig` pipeline is `mergeConfig → applyEnvOverrides → resolveSecrets`. The `apiKeyCommand` config field shells out to an external secret manager via `execFileSync` (no shell). Priority: command output > env var > file config > defaults. On failure, warns and falls back gracefully
 
+**Configuration:** All tunable behavioral constants live in `DEFAULTS` in `src/infrastructure/config.js`, grouped by concern (`analysis`, `risk`, `search`, `display`, `community`, `structure`, `mcp`, `check`, `coChange`, `manifesto`). Users override via `.codegraphrc.json` — `mergeConfig` deep-merges recursively so partial overrides preserve sibling keys. Env vars override LLM settings (`CODEGRAPH_LLM_*`). When adding new behavioral constants, **always add them to `DEFAULTS`** and wire them through config — never introduce new hardcoded magic numbers in individual modules. Category F values (safety boundaries, standard formulas, platform concerns) are the only exception.
+
 **Database:** SQLite at `.codegraph/graph.db` with tables: `nodes`, `edges`, `metadata`, `embeddings`, `function_complexity`
 
 ## Test Structure
diff --git a/src/domain/analysis/brief.js b/src/domain/analysis/brief.js
index c472afcbf..78c3d3420 100644
--- a/src/domain/analysis/brief.js
+++ b/src/domain/analysis/brief.js
@@ -7,6 +7,7 @@ import {
   findNodesByFile,
   openReadonlyOrFail,
 } from '../../db/index.js';
+import { loadConfig } from '../../infrastructure/config.js';
 import { isTestFile } from '../../infrastructure/test-filter.js';
 
 /** Symbol kinds meaningful for a file brief — excludes parameters, properties, constants. */
@@ -28,15 +29,15 @@ const BRIEF_KINDS = new Set([
  * @param {{ role: string|null, callerCount: number }[]} symbols
  * @returns {'high'|'medium'|'low'}
  */
-function computeRiskTier(symbols) {
+function computeRiskTier(symbols, highThreshold = 10, mediumThreshold = 3) {
   let maxCallers = 0;
   let hasCoreRole = false;
   for (const s of symbols) {
     if (s.callerCount > maxCallers) maxCallers = s.callerCount;
     if (s.role === 'core') hasCoreRole = true;
   }
-  if (maxCallers >= 10 || hasCoreRole) return 'high';
-  if (maxCallers >= 3) return 'medium';
+  if (maxCallers >= highThreshold || hasCoreRole) return 'high';
+  if (maxCallers >= mediumThreshold) return 'medium';
   return 'low';
 }
 
@@ -105,6 +106,11 @@ export function briefData(file, customDbPath, opts = {}) {
   const db = openReadonlyOrFail(customDbPath);
   try {
     const noTests = opts.noTests || false;
+    const config = opts.config || loadConfig();
+    const callerDepth = config.analysis?.briefCallerDepth ?? 5;
+    const importerDepth = config.analysis?.briefImporterDepth ?? 5;
+    const highRiskCallers = config.analysis?.briefHighRiskCallers ?? 10;
+    const mediumRiskCallers = config.analysis?.briefMediumRiskCallers ?? 3;
     const fileNodes = findFileNodes(db, `%${file}%`);
     if (fileNodes.length === 0) {
       return { file, results: [] };
@@ -117,7 +123,7 @@ export function briefData(file, customDbPath, opts = {}) {
       const directImporters = [...new Set(importedBy.map((i) => i.file))];
 
       // Transitive importer count
-      const totalImporterCount = countTransitiveImporters(db, [fn.id], noTests);
+      const totalImporterCount = countTransitiveImporters(db, [fn.id], noTests, importerDepth);
 
       // Direct imports
       let importsTo = findImportTargets(db, fn.id);
@@ -126,7 +132,7 @@ export function briefData(file, customDbPath, opts = {}) {
       // Symbol definitions with roles and caller counts
       const defs = findNodesByFile(db, fn.file).filter((d) => BRIEF_KINDS.has(d.kind));
       const symbols = defs.map((d) => {
-        const callerCount = countTransitiveCallers(db, d.id, noTests);
+        const callerCount = countTransitiveCallers(db, d.id, noTests, callerDepth);
         return {
           name: d.name,
           kind: d.kind,
@@ -136,7 +142,7 @@ export function briefData(file, customDbPath, opts = {}) {
         };
       });
 
-      const riskTier = computeRiskTier(symbols);
+      const riskTier = computeRiskTier(symbols, highRiskCallers, mediumRiskCallers);
 
       return {
         file: fn.file,
diff --git a/src/domain/analysis/context.js b/src/domain/analysis/context.js
index e8b5a8691..516d08422 100644
--- a/src/domain/analysis/context.js
+++ b/src/domain/analysis/context.js
@@ -13,6 +13,7 @@ import {
   getComplexityForNode,
   openReadonlyOrFail,
 } from '../../db/index.js';
+import { loadConfig } from '../../infrastructure/config.js';
 import { debug } from '../../infrastructure/logger.js';
 import { isTestFile } from '../../infrastructure/test-filter.js';
 import {
@@ -28,16 +29,16 @@ import { paginateResult } from '../../shared/paginate.js';
 import { findMatchingNodes } from './symbol-lookup.js';
 
 function buildCallees(db, node, repoRoot, getFileLines, opts) {
-  const { noTests, depth } = opts;
+  const { noTests, depth, displayOpts } = opts;
   const calleeRows = findCallees(db, node.id);
   const filteredCallees = noTests ? calleeRows.filter((c) => !isTestFile(c.file)) : calleeRows;
 
   const callees = filteredCallees.map((c) => {
     const cLines = getFileLines(c.file);
-    const summary = cLines ? extractSummary(cLines, c.line) : null;
+    const summary = cLines ? extractSummary(cLines, c.line, displayOpts) : null;
     let calleeSource = null;
     if (depth >= 1) {
-      calleeSource = readSourceRange(repoRoot, c.file, c.line, c.end_line);
+      calleeSource = readSourceRange(repoRoot, c.file, c.line, c.end_line, displayOpts);
     }
     return {
       name: c.name,
@@ -70,8 +71,8 @@ function buildCallees(db, node, repoRoot, getFileLines, opts) {
               file: c.file,
               line: c.line,
               endLine: c.end_line || null,
-              summary: cLines ? extractSummary(cLines, c.line) : null,
-              source: readSourceRange(repoRoot, c.file, c.line, c.end_line),
+              summary: cLines ? extractSummary(cLines, c.line, displayOpts) : null,
+              source: readSourceRange(repoRoot, c.file, c.line, c.end_line, displayOpts),
             });
           }
         }
@@ -170,7 +171,7 @@ function getNodeChildrenSafe(db, nodeId) {
   }
 }
 
-function explainFileImpl(db, target, getFileLines) {
+function explainFileImpl(db, target, getFileLines, displayOpts) {
   const fileNodes = findFileNodes(db, `%${target}%`);
   if (fileNodes.length === 0) return [];
 
@@ -186,8 +187,8 @@ function explainFileImpl(db, target, getFileLines) {
       kind: s.kind,
       line: s.line,
       role: s.role || null,
-      summary: fileLines ? extractSummary(fileLines, s.line) : null,
-      signature: fileLines ? extractSignature(fileLines, s.line) : null,
+      summary: fileLines ? extractSummary(fileLines, s.line, displayOpts) : null,
+      signature: fileLines ? extractSignature(fileLines, s.line, displayOpts) : null,
     });
 
     const publicApi = symbols.filter((s) => publicIds.has(s.id)).map(mapSymbol);
@@ -231,7 +232,7 @@ function explainFileImpl(db, target, getFileLines) {
   });
 }
 
-function explainFunctionImpl(db, target, noTests, getFileLines) {
+function explainFunctionImpl(db, target, noTests, getFileLines, displayOpts) {
   let nodes = db
     .prepare(
       `SELECT * FROM nodes WHERE name LIKE ? AND kind IN ('function','method','class','interface','type','struct','enum','trait','record','module','constant') ORDER BY file, line`,
@@ -244,8 +245,8 @@ function explainFunctionImpl(db, target, noTests, getFileLines) {
   return nodes.slice(0, 10).map((node) => {
     const fileLines = getFileLines(node.file);
     const lineCount = node.end_line ? node.end_line - node.line + 1 : null;
-    const summary = fileLines ? extractSummary(fileLines, node.line) : null;
-    const signature = fileLines ? extractSignature(fileLines, node.line) : null;
+    const summary = fileLines ? extractSummary(fileLines, node.line, displayOpts) : null;
+    const signature = fileLines ? extractSignature(fileLines, node.line, displayOpts) : null;
 
     const callees = findCallees(db, node.id).map((c) => ({
       name: c.name,
@@ -281,7 +282,15 @@ function explainFunctionImpl(db, target, noTests, getFileLines) {
   });
 }
 
-function explainCallees(parentResults, currentDepth, visited, db, noTests, getFileLines) {
+function explainCallees(
+  parentResults,
+  currentDepth,
+  visited,
+  db,
+  noTests,
+  getFileLines,
+  displayOpts,
+) {
   if (currentDepth <= 0) return;
   for (const r of parentResults) {
     const newCallees = [];
@@ -289,7 +298,13 @@ function explainCallees(parentResults, currentDepth, visited, db, noTests, getFi
       const key = `${callee.name}:${callee.file}:${callee.line}`;
       if (visited.has(key)) continue;
       visited.add(key);
-      const calleeResults = explainFunctionImpl(db, callee.name, noTests, getFileLines);
+      const calleeResults = explainFunctionImpl(
+        db,
+        callee.name,
+        noTests,
+        getFileLines,
+        displayOpts,
+      );
       const exact = calleeResults.find((cr) => cr.file === callee.file && cr.line === callee.line);
       if (exact) {
         exact._depth = (r._depth || 0) + 1;
@@ -298,7 +313,7 @@ function explainCallees(parentResults, currentDepth, visited, db, noTests, getFi
     }
     if (newCallees.length > 0) {
       r.depDetails = newCallees;
-      explainCallees(newCallees, currentDepth - 1, visited, db, noTests, getFileLines);
+      explainCallees(newCallees, currentDepth - 1, visited, db, noTests, getFileLines, displayOpts);
     }
   }
 }
@@ -313,6 +328,9 @@ export function contextData(name, customDbPath, opts = {}) {
     const noTests = opts.noTests || false;
     const includeTests = opts.includeTests || false;
 
+    const config = opts.config || loadConfig();
+    const displayOpts = config.display || {};
+
     const dbPath = findDbPath(customDbPath);
     const repoRoot = path.resolve(path.dirname(dbPath), '..');
 
@@ -328,11 +346,15 @@ export function contextData(name, customDbPath, opts = {}) {
 
       const source = noSource
         ? null
-        : readSourceRange(repoRoot, node.file, node.line, node.end_line);
+        : readSourceRange(repoRoot, node.file, node.line, node.end_line, displayOpts);
 
-      const signature = fileLines ? extractSignature(fileLines, node.line) : null;
+      const signature = fileLines ? extractSignature(fileLines, node.line, displayOpts) : null;
 
-      const callees = buildCallees(db, node, repoRoot, getFileLines, { noTests, depth });
+      const callees = buildCallees(db, node, repoRoot, getFileLines, {
+        noTests,
+        depth,
+        displayOpts,
+      });
       const callers = buildCallers(db, node, noTests);
       const relatedTests = buildRelatedTests(db, node, getFileLines, includeTests);
       const complexityMetrics = getComplexityMetrics(db, node.id);
@@ -369,6 +391,9 @@ export function explainData(target, customDbPath, opts = {}) {
     const depth = opts.depth || 0;
     const kind = isFileLikeTarget(target) ? 'file' : 'function';
 
+    const config = opts.config || loadConfig();
+    const displayOpts = config.display || {};
+
     const dbPath = findDbPath(customDbPath);
     const repoRoot = path.resolve(path.dirname(dbPath), '..');
 
@@ -376,12 +401,12 @@ export function explainData(target, customDbPath, opts = {}) {
 
     const results =
       kind === 'file'
-        ? explainFileImpl(db, target, getFileLines)
-        : explainFunctionImpl(db, target, noTests, getFileLines);
+        ? explainFileImpl(db, target, getFileLines, displayOpts)
+        : explainFunctionImpl(db, target, noTests, getFileLines, displayOpts);
 
     if (kind === 'function' && depth > 0 && results.length > 0) {
       const visited = new Set(results.map((r) => `${r.name}:${r.file}:${r.line}`));
-      explainCallees(results, depth, visited, db, noTests, getFileLines);
+      explainCallees(results, depth, visited, db, noTests, getFileLines, displayOpts);
     }
 
     const base = { target, kind, results };
diff --git a/src/domain/analysis/exports.js b/src/domain/analysis/exports.js
index 7bebac406..7c086d6e6 100644
--- a/src/domain/analysis/exports.js
+++ b/src/domain/analysis/exports.js
@@ -6,6 +6,7 @@ import {
   findNodesByFile,
   openReadonlyOrFail,
 } from '../../db/index.js';
+import { loadConfig } from '../../infrastructure/config.js';
 import { debug } from '../../infrastructure/logger.js';
 import { isTestFile } from '../../infrastructure/test-filter.js';
 import {
@@ -20,13 +21,16 @@ export function exportsData(file, customDbPath, opts = {}) {
   try {
     const noTests = opts.noTests || false;
 
+    const config = opts.config || loadConfig();
+    const displayOpts = config.display || {};
+
     const dbFilePath = findDbPath(customDbPath);
     const repoRoot = path.resolve(path.dirname(dbFilePath), '..');
 
     const getFileLines = createFileLinesReader(repoRoot);
 
     const unused = opts.unused || false;
-    const fileResults = exportsFileImpl(db, file, noTests, getFileLines, unused);
+    const fileResults = exportsFileImpl(db, file, noTests, getFileLines, unused, displayOpts);
 
     if (fileResults.length === 0) {
       return paginateResult(
@@ -52,7 +56,7 @@ export function exportsData(file, customDbPath, opts = {}) {
   }
 }
 
-function exportsFileImpl(db, target, noTests, getFileLines, unused) {
+function exportsFileImpl(db, target, noTests, getFileLines, unused, displayOpts) {
   const fileNodes = findFileNodes(db, `%${target}%`);
   if (fileNodes.length === 0) return [];
 
@@ -100,8 +104,8 @@ function exportsFileImpl(db, target, noTests, getFileLines, unused) {
         line: s.line,
         endLine: s.end_line ?? null,
         role: s.role || null,
-        signature: fileLines ? extractSignature(fileLines, s.line) : null,
-        summary: fileLines ? extractSummary(fileLines, s.line) : null,
+        signature: fileLines ? extractSignature(fileLines, s.line, displayOpts) : null,
+        summary: fileLines ? extractSummary(fileLines, s.line, displayOpts) : null,
         consumers: consumers.map((c) => ({ name: c.name, file: c.file, line: c.line })),
         consumerCount: consumers.length,
       };
diff --git a/src/domain/analysis/impact.js b/src/domain/analysis/impact.js
index 6bdd5464e..413ce3330 100644
--- a/src/domain/analysis/impact.js
+++ b/src/domain/analysis/impact.js
@@ -109,7 +109,8 @@ export function impactAnalysisData(file, customDbPath, opts = {}) {
 export function fnImpactData(name, customDbPath, opts = {}) {
   const db = openReadonlyOrFail(customDbPath);
   try {
-    const maxDepth = opts.depth || 5;
+    const config = opts.config || loadConfig();
+    const maxDepth = opts.depth || config.analysis?.fnImpactDepth || 5;
     const noTests = opts.noTests || false;
     const hc = new Map();
 
@@ -387,7 +388,8 @@ export function diffImpactData(customDbPath, opts = {}) {
   const db = openReadonlyOrFail(customDbPath);
   try {
     const noTests = opts.noTests || false;
-    const maxDepth = opts.depth || 3;
+    const config = opts.config || loadConfig();
+    const maxDepth = opts.depth || config.analysis?.impactDepth || 3;
 
     const dbPath = findDbPath(customDbPath);
     const repoRoot = path.resolve(path.dirname(dbPath), '..');
diff --git a/src/domain/analysis/module-map.js b/src/domain/analysis/module-map.js
index 5cf4c47f5..d3566c8c6 100644
--- a/src/domain/analysis/module-map.js
+++ b/src/domain/analysis/module-map.js
@@ -1,5 +1,6 @@
 import path from 'node:path';
 import { openReadonlyOrFail, testFilterSQL } from '../../db/index.js';
+import { loadConfig } from '../../infrastructure/config.js';
 import { debug } from '../../infrastructure/logger.js';
 import { isTestFile } from '../../infrastructure/test-filter.js';
 import { DEAD_ROLE_PREFIX } from '../../shared/kinds.js';
@@ -160,7 +161,7 @@ function getEmbeddingsInfo(db) {
   return null;
 }
 
-function computeQualityMetrics(db, testFilter) {
+function computeQualityMetrics(db, testFilter, fpThreshold = FALSE_POSITIVE_CALLER_THRESHOLD) {
   const qualityTestFilter = testFilter.replace(/n\.file/g, 'file');
 
   const totalCallable = db
@@ -193,7 +194,7 @@ function computeQualityMetrics(db, testFilter) {
       HAVING caller_count > ?
       ORDER BY caller_count DESC
     `)
-    .all(FALSE_POSITIVE_CALLER_THRESHOLD);
+    .all(fpThreshold);
   const falsePositiveWarnings = fpRows
     .filter((r) =>
       FALSE_POSITIVE_NAMES.has(r.name.includes('.') ? r.name.split('.').pop() : r.name),
@@ -320,6 +321,7 @@ export function statsData(customDbPath, opts = {}) {
   const db = openReadonlyOrFail(customDbPath);
   try {
     const noTests = opts.noTests || false;
+    const config = opts.config || loadConfig();
     const testFilter = testFilterSQL('n.file', noTests);
 
     const testFileIds = noTests ? buildTestFileIds(db) : null;
@@ -333,7 +335,8 @@ export function statsData(customDbPath, opts = {}) {
 
     const hotspots = findHotspots(db, noTests, 5);
     const embeddings = getEmbeddingsInfo(db);
-    const quality = computeQualityMetrics(db, testFilter);
+    const fpThreshold = config.analysis?.falsePositiveCallers ?? FALSE_POSITIVE_CALLER_THRESHOLD;
+    const quality = computeQualityMetrics(db, testFilter, fpThreshold);
     const roles = countRoles(db, noTests);
     const complexity = getComplexitySummary(db, testFilter);
 
diff --git a/src/domain/search/search/hybrid.js b/src/domain/search/search/hybrid.js
index 6d2365683..2c6cd00a2 100644
--- a/src/domain/search/search/hybrid.js
+++ b/src/domain/search/search/hybrid.js
@@ -1,4 +1,5 @@
 import { openReadonlyOrFail } from '../../../db/index.js';
+import { loadConfig } from '../../../infrastructure/config.js';
 import { hasFtsIndex } from '../stores/fts5.js';
 import { ftsSearchData } from './keyword.js';
 import { searchData } from './semantic.js';
@@ -9,9 +10,11 @@ import { searchData } from './semantic.js';
  * or null if no FTS5 index (caller should fall back to semantic-only).
  */
 export async function hybridSearchData(query, customDbPath, opts = {}) {
-  const limit = opts.limit || 15;
-  const k = opts.rrfK || 60;
-  const topK = (opts.limit || 15) * 5;
+  const config = opts.config || loadConfig();
+  const searchCfg = config.search || {};
+  const limit = opts.limit ?? searchCfg.topK ?? 15;
+  const k = opts.rrfK ?? searchCfg.rrfK ?? 60;
+  const topK = (opts.limit ?? searchCfg.topK ?? 15) * 5;
 
   // Split semicolons for multi-query support
   const queries =
@@ -49,7 +52,7 @@ export async function hybridSearchData(query, customDbPath, opts = {}) {
     const semData = await searchData(q, customDbPath, {
       ...opts,
       limit: topK,
-      minScore: opts.minScore || 0.2,
+      minScore: opts.minScore ?? 0.2,
     });
     if (semData?.results) {
       rankedLists.push(
diff --git a/src/domain/search/search/semantic.js b/src/domain/search/search/semantic.js
index dc7b301ab..262d59461 100644
--- a/src/domain/search/search/semantic.js
+++ b/src/domain/search/search/semantic.js
@@ -1,3 +1,4 @@
+import { loadConfig } from '../../../infrastructure/config.js';
 import { warn } from '../../../infrastructure/logger.js';
 import { normalizeSymbol } from '../../queries.js';
 import { embed } from '../models.js';
@@ -9,8 +10,10 @@ import { prepareSearch } from './prepare.js';
  * Returns { results: [{ name, kind, file, line, similarity }] } or null on failure.
  */
 export async function searchData(query, customDbPath, opts = {}) {
-  const limit = opts.limit || 15;
-  const minScore = opts.minScore || 0.2;
+  const config = opts.config || loadConfig();
+  const searchCfg = config.search || {};
+  const limit = opts.limit ?? searchCfg.topK ?? 15;
+  const minScore = opts.minScore ?? searchCfg.defaultMinScore ?? 0.2;
 
   const prepared = prepareSearch(customDbPath, opts);
   if (!prepared) return null;
@@ -56,9 +59,11 @@ export async function searchData(query, customDbPath, opts = {}) {
  * Returns { results: [{ name, kind, file, line, rrf, queryScores }] } or null on failure.
  */
 export async function multiSearchData(queries, customDbPath, opts = {}) {
-  const limit = opts.limit || 15;
-  const minScore = opts.minScore || 0.2;
-  const k = opts.rrfK || 60;
+  const config = opts.config || loadConfig();
+  const searchCfg = config.search || {};
+  const limit = opts.limit ?? searchCfg.topK ?? 15;
+  const minScore = opts.minScore ?? searchCfg.defaultMinScore ?? 0.2;
+  const k = opts.rrfK ?? searchCfg.rrfK ?? 60;
 
   const prepared = prepareSearch(customDbPath, opts);
   if (!prepared) return null;
@@ -68,7 +73,7 @@ export async function multiSearchData(queries, customDbPath, opts = {}) {
     const { vectors: queryVecs, dim } = await embed(queries, modelKey);
 
     // Warn about similar queries that may bias RRF results
-    const SIMILARITY_WARN_THRESHOLD = 0.85;
+    const SIMILARITY_WARN_THRESHOLD = searchCfg.similarityWarnThreshold ?? 0.85;
     for (let i = 0; i < queryVecs.length; i++) {
       for (let j = i + 1; j < queryVecs.length; j++) {
         const sim = cosineSim(queryVecs[i], queryVecs[j]);
diff --git a/src/features/audit.js b/src/features/audit.js
index 5cc74a6c9..b9bddb2bd 100644
--- a/src/features/audit.js
+++ b/src/features/audit.js
@@ -100,7 +100,8 @@ function readPhase44(db, nodeId) {
 
 export function auditData(target, customDbPath, opts = {}) {
   const noTests = opts.noTests || false;
-  const maxDepth = opts.depth || 3;
+  const config = opts.config || loadConfig();
+  const maxDepth = opts.depth || config.analysis?.auditDepth || 3;
   const fileFilters = normalizeFileFilter(opts.file);
   const kind = opts.kind;
 
diff --git a/src/features/communities.js b/src/features/communities.js
index f850dc8d5..1f3a54d71 100644
--- a/src/features/communities.js
+++ b/src/features/communities.js
@@ -2,6 +2,7 @@ import path from 'node:path';
 import { openRepo } from '../db/index.js';
 import { louvainCommunities } from '../graph/algorithms/louvain.js';
 import { buildDependencyGraph } from '../graph/builders/dependency.js';
+import { loadConfig } from '../infrastructure/config.js';
 import { paginateResult } from '../shared/paginate.js';
 
 // ─── Directory Helpers ────────────────────────────────────────────────
@@ -144,7 +145,8 @@ export function communitiesData(customDbPath, opts = {}) {
     };
   }
 
-  const resolution = opts.resolution ?? 1.0;
+  const config = opts.config || loadConfig();
+  const resolution = opts.resolution ?? config.community?.resolution ?? 1.0;
   const { assignments, modularity } = louvainCommunities(graph, { resolution });
 
   const { communities, communityDirs } = buildCommunityObjects(graph, assignments, opts);
diff --git a/src/features/sequence.js b/src/features/sequence.js
index cf59ddc33..8fd5a74f1 100644
--- a/src/features/sequence.js
+++ b/src/features/sequence.js
@@ -9,6 +9,7 @@
 import { openRepo } from '../db/index.js';
 import { SqliteRepository } from '../db/repository/sqlite-repository.js';
 import { findMatchingNodes } from '../domain/queries.js';
+import { loadConfig } from '../infrastructure/config.js';
 import { isTestFile } from '../infrastructure/test-filter.js';
 import { paginateResult } from '../shared/paginate.js';
 import { FRAMEWORK_ENTRY_PREFIXES } from './structure.js';
@@ -230,7 +231,8 @@ function buildParticipants(fileSet, entryFile) {
 export function sequenceData(name, dbPath, opts = {}) {
   const { repo, close } = openRepo(dbPath, opts);
   try {
-    const maxDepth = opts.depth || 10;
+    const config = opts.config || loadConfig();
+    const maxDepth = opts.depth || config.analysis?.sequenceDepth || 10;
     const noTests = opts.noTests || false;
 
     const matchNode = findEntryNode(repo, name, opts);
diff --git a/src/features/structure.js b/src/features/structure.js
index 87dfc6a23..cfbf0e4c4 100644
--- a/src/features/structure.js
+++ b/src/features/structure.js
@@ -1,5 +1,6 @@
 import path from 'node:path';
 import { getNodeId, openReadonlyOrFail, testFilterSQL } from '../db/index.js';
+import { loadConfig } from '../infrastructure/config.js';
 import { debug } from '../infrastructure/logger.js';
 import { isTestFile } from '../infrastructure/test-filter.js';
 import { normalizePath } from '../shared/constants.js';
@@ -636,7 +637,8 @@ export function hotspotsData(customDbPath, opts = {}) {
 export function moduleBoundariesData(customDbPath, opts = {}) {
   const db = openReadonlyOrFail(customDbPath);
   try {
-    const threshold = opts.threshold || 0.3;
+    const config = opts.config || loadConfig();
+    const threshold = opts.threshold ?? config.structure?.cohesionThreshold ?? 0.3;
 
     const dirs = db
       .prepare(`
diff --git a/src/features/triage.js b/src/features/triage.js
index 8c23875a7..7b7d36046 100644
--- a/src/features/triage.js
+++ b/src/features/triage.js
@@ -1,5 +1,6 @@
 import { openRepo } from '../db/index.js';
 import { DEFAULT_WEIGHTS, scoreRisk } from '../graph/classifiers/risk.js';
+import { loadConfig } from '../infrastructure/config.js';
 import { warn } from '../infrastructure/logger.js';
 import { isTestFile } from '../infrastructure/test-filter.js';
 import { paginateResult } from '../shared/paginate.js';
@@ -94,7 +95,13 @@ export function triageData(customDbPath, opts = {}) {
     const noTests = opts.noTests || false;
     const minScore = opts.minScore != null ? Number(opts.minScore) : null;
     const sort = opts.sort || 'risk';
-    const weights = { ...DEFAULT_WEIGHTS, ...(opts.weights || {}) };
+    const config = opts.config || loadConfig();
+    const riskConfig = config.risk || {};
+    const weights = { ...DEFAULT_WEIGHTS, ...(riskConfig.weights || {}), ...(opts.weights || {}) };
+    const riskOpts = {
+      roleWeights: riskConfig.roleWeights,
+      defaultRoleWeight: riskConfig.defaultRoleWeight,
+    };
 
     let rows;
     try {
@@ -114,7 +121,7 @@ export function triageData(customDbPath, opts = {}) {
       return { items: [], summary: EMPTY_SUMMARY(weights) };
     }
 
-    const riskMetrics = scoreRisk(filtered, weights);
+    const riskMetrics = scoreRisk(filtered, weights, riskOpts);
     const items = buildTriageItems(filtered, riskMetrics);
 
     const scored = minScore != null ? items.filter((it) => it.riskScore >= minScore) : items;
diff --git a/src/graph/classifiers/risk.js b/src/graph/classifiers/risk.js
index 930776faa..0ef67c08a 100644
--- a/src/graph/classifiers/risk.js
+++ b/src/graph/classifiers/risk.js
@@ -52,11 +52,14 @@ function round4(n) {
  *
  * @param {{ fan_in: number, cognitive: number, churn: number, mi: number, role: string|null }[]} items
  * @param {object} [weights] - Override DEFAULT_WEIGHTS
+ * @param {{ roleWeights?: object, defaultRoleWeight?: number }} [opts] - Optional role weight overrides
  * @returns {{ normFanIn: number, normComplexity: number, normChurn: number, normMI: number, roleWeight: number, riskScore: number }[]}
  *   Parallel array with risk metrics for each input item.
  */
-export function scoreRisk(items, weights = {}) {
+export function scoreRisk(items, weights = {}, opts = {}) {
   const w = { ...DEFAULT_WEIGHTS, ...weights };
+  const rw = opts.roleWeights || ROLE_WEIGHTS;
+  const drw = opts.defaultRoleWeight ?? DEFAULT_ROLE_WEIGHT;
 
   const fanIns = items.map((r) => r.fan_in);
   const cognitives = items.map((r) => r.cognitive);
@@ -70,7 +73,7 @@ export function scoreRisk(items, weights = {}) {
   const normMIs = normMIsRaw.map((v) => round4(1 - v));
 
   return items.map((r, i) => {
-    const roleWeight = ROLE_WEIGHTS[r.role] ?? DEFAULT_ROLE_WEIGHT;
+    const roleWeight = rw[r.role] ?? drw;
     const riskScore =
       w.fanIn * normFanIns[i] +
       w.complexity * normCognitives[i] +
diff --git a/src/infrastructure/config.js b/src/infrastructure/config.js
index 1ab75e47f..1e3eb41ec 100644
--- a/src/infrastructure/config.js
+++ b/src/infrastructure/config.js
@@ -23,7 +23,7 @@ export const DEFAULTS = {
   },
   embeddings: { model: 'nomic-v1.5', llmProvider: null },
   llm: { provider: null, model: null, baseUrl: null, apiKey: null, apiKeyCommand: null },
-  search: { defaultMinScore: 0.2, rrfK: 60, topK: 15 },
+  search: { defaultMinScore: 0.2, rrfK: 60, topK: 15, similarityWarnThreshold: 0.85 },
   ci: { failOnCycles: false, impactThreshold: null },
   manifesto: {
     rules: {
@@ -54,6 +54,80 @@ export const DEFAULTS = {
     minJaccard: 0.3,
     maxFilesPerCommit: 50,
   },
+  analysis: {
+    impactDepth: 3,
+    fnImpactDepth: 5,
+    auditDepth: 3,
+    sequenceDepth: 10,
+    falsePositiveCallers: 20,
+    briefCallerDepth: 5,
+    briefImporterDepth: 5,
+    briefHighRiskCallers: 10,
+    briefMediumRiskCallers: 3,
+  },
+  community: {
+    resolution: 1.0,
+  },
+  structure: {
+    cohesionThreshold: 0.3,
+  },
+  risk: {
+    weights: {
+      fanIn: 0.25,
+      complexity: 0.3,
+      churn: 0.2,
+      role: 0.15,
+      mi: 0.1,
+    },
+    roleWeights: {
+      core: 1.0,
+      utility: 0.9,
+      entry: 0.8,
+      adapter: 0.5,
+      leaf: 0.2,
+      'test-only': 0.1,
+      dead: 0.1,
+      'dead-leaf': 0.0,
+      'dead-entry': 0.3,
+      'dead-ffi': 0.05,
+      'dead-unresolved': 0.15,
+    },
+    defaultRoleWeight: 0.5,
+  },
+  display: {
+    maxColWidth: 40,
+    excerptLines: 50,
+    summaryMaxChars: 100,
+    jsdocEndScanLines: 10,
+    jsdocOpenScanLines: 20,
+    signatureGatherLines: 5,
+  },
+  mcp: {
+    defaults: {
+      list_functions: 100,
+      query: 10,
+      where: 50,
+      node_roles: 100,
+      export_graph: 500,
+      fn_impact: 5,
+      context: 5,
+      explain: 10,
+      file_deps: 20,
+      file_exports: 20,
+      diff_impact: 30,
+      impact_analysis: 20,
+      semantic_search: 20,
+      execution_flow: 50,
+      hotspots: 20,
+      co_changes: 20,
+      complexity: 30,
+      manifesto: 50,
+      communities: 20,
+      structure: 30,
+      triage: 20,
+      ast_query: 50,
+    },
+  },
 };
 
 /**
@@ -120,7 +194,7 @@ export function resolveSecrets(config) {
   return config;
 }
 
-function mergeConfig(defaults, overrides) {
+export function mergeConfig(defaults, overrides) {
   const result = { ...defaults };
   for (const [key, value] of Object.entries(overrides)) {
     if (
@@ -128,9 +202,10 @@ function mergeConfig(defaults, overrides) {
       typeof value === 'object' &&
       !Array.isArray(value) &&
       defaults[key] &&
-      typeof defaults[key] === 'object'
+      typeof defaults[key] === 'object' &&
+      !Array.isArray(defaults[key])
     ) {
-      result[key] = { ...defaults[key], ...value };
+      result[key] = mergeConfig(defaults[key], value);
     } else {
       result[key] = value;
     }
diff --git a/src/mcp/middleware.js b/src/mcp/middleware.js
index 96dc26aff..01bb8ed2f 100644
--- a/src/mcp/middleware.js
+++ b/src/mcp/middleware.js
@@ -2,10 +2,28 @@
  * MCP middleware helpers — pagination defaults and limits.
  */
 
-import { MCP_DEFAULTS, MCP_MAX_LIMIT } from '../shared/paginate.js';
+import { getMcpDefaults, MCP_DEFAULTS, MCP_MAX_LIMIT } from '../shared/paginate.js';
 
 export { MCP_DEFAULTS, MCP_MAX_LIMIT };
 
+/** Resolved MCP defaults (may include config overrides). Set via initMcpDefaults(). */
+let resolvedDefaults = MCP_DEFAULTS;
+
+/**
+ * Initialize MCP defaults from config. Call once at server startup.
+ * @param {object} [configMcpDefaults] - config.mcp.defaults overrides
+ */
+export function initMcpDefaults(configMcpDefaults) {
+  resolvedDefaults = getMcpDefaults(configMcpDefaults);
+}
+
+/**
+ * Reset MCP defaults back to the base defaults. Useful for test isolation.
+ */
+export function resetMcpDefaults() {
+  resolvedDefaults = MCP_DEFAULTS;
+}
+
 /**
  * Resolve effective limit for a tool call.
  * @param {object} args - Tool arguments
@@ -13,7 +31,7 @@ export { MCP_DEFAULTS, MCP_MAX_LIMIT };
  * @returns {number}
  */
 export function effectiveLimit(args, toolName) {
-  return Math.min(args.limit ?? MCP_DEFAULTS[toolName] ?? 100, MCP_MAX_LIMIT);
+  return Math.min(args.limit ?? resolvedDefaults[toolName] ?? 100, MCP_MAX_LIMIT);
 }
 
 /**
diff --git a/src/mcp/server.js b/src/mcp/server.js
index bae0bbbf4..db5d3eb8d 100644
--- a/src/mcp/server.js
+++ b/src/mcp/server.js
@@ -7,8 +7,10 @@
 
 import { createRequire } from 'node:module';
 import { findDbPath } from '../db/index.js';
+import { loadConfig } from '../infrastructure/config.js';
 import { CodegraphError, ConfigError } from '../shared/errors.js';
 import { MCP_MAX_LIMIT } from '../shared/paginate.js';
+import { initMcpDefaults } from './middleware.js';
 import { buildToolList } from './tool-registry.js';
 import { TOOL_HANDLERS } from './tools/index.js';
 
@@ -91,6 +93,10 @@ export async function startMCPServer(customDbPath, options = {}) {
   const { allowedRepos } = options;
   const multiRepo = options.multiRepo || !!allowedRepos;
 
+  // Apply config-based MCP page-size overrides
+  const config = options.config || loadConfig();
+  initMcpDefaults(config.mcp?.defaults);
+
   const { Server, StdioServerTransport, ListToolsRequestSchema, CallToolRequestSchema } =
     await loadMCPSdk();
 
diff --git a/src/presentation/result-formatter.js b/src/presentation/result-formatter.js
index 7565115b7..b3fc843d0 100644
--- a/src/presentation/result-formatter.js
+++ b/src/presentation/result-formatter.js
@@ -1,3 +1,4 @@
+import { loadConfig } from '../infrastructure/config.js';
 import { printNdjson } from '../shared/paginate.js';
 import { formatTable, truncEnd } from './table.js';
 
@@ -85,11 +86,13 @@ const MAX_COL_WIDTH = 40;
  * Print data as an aligned table to stdout.
  * @param {object} data - Result object from a *Data() function
  * @param {string} field - Array field name (e.g. 'results')
+ * @param {{ maxColWidth?: number }} [displayOpts]
  */
-function printAutoTable(data, field) {
+function printAutoTable(data, field, displayOpts = {}) {
   const prepared = prepareFlatItems(data, field);
   if (!prepared) return false;
   const { flatItems, columns } = prepared;
+  const colWidth = displayOpts.maxColWidth ?? MAX_COL_WIDTH;
 
   const colDefs = columns.map((col) => {
     const maxLen = flatItems.reduce(
@@ -104,13 +107,13 @@ function printAutoTable(data, field) {
       });
     return {
       header: col,
-      width: Math.min(maxLen, MAX_COL_WIDTH),
+      width: Math.min(maxLen, colWidth),
       align: isNumeric ? 'right' : 'left',
     };
   });
 
   const rows = flatItems.map((item) =>
-    columns.map((col) => truncEnd(String(item[col] ?? ''), MAX_COL_WIDTH)),
+    columns.map((col) => truncEnd(String(item[col] ?? ''), colWidth)),
   );
 
   console.log(formatTable({ columns: colDefs, rows }));
@@ -122,7 +125,7 @@ function printAutoTable(data, field) {
  *
  * @param {object} data   - Result object from a *Data() function
  * @param {string} field  - Array field name for NDJSON streaming (e.g. 'results')
- * @param {object} opts   - CLI options ({ json?, ndjson?, table?, csv? })
+ * @param {object} opts   - CLI options ({ json?, ndjson?, table?, csv?, display?: { maxColWidth? } })
  * @returns {boolean} true if output was handled (caller should return early)
  */
 export function outputResult(data, field, opts) {
@@ -138,7 +141,8 @@ export function outputResult(data, field, opts) {
     return printCsv(data, field) !== false;
   }
   if (opts.table) {
-    return printAutoTable(data, field) !== false;
+    const displayOpts = opts.display ?? loadConfig().display;
+    return printAutoTable(data, field, displayOpts) !== false;
   }
   return false;
 }
diff --git a/src/shared/file-utils.js b/src/shared/file-utils.js
index 814f54de0..c48ae9cbe 100644
--- a/src/shared/file-utils.js
+++ b/src/shared/file-utils.js
@@ -13,14 +13,15 @@ export function safePath(repoRoot, file) {
   return resolved;
 }
 
-export function readSourceRange(repoRoot, file, startLine, endLine) {
+export function readSourceRange(repoRoot, file, startLine, endLine, opts = {}) {
   try {
     const absPath = safePath(repoRoot, file);
     if (!absPath) return null;
     const content = fs.readFileSync(absPath, 'utf-8');
     const lines = content.split('\n');
+    const excerptLines = opts.excerptLines ?? 50;
     const start = Math.max(0, (startLine || 1) - 1);
-    const end = Math.min(lines.length, endLine || startLine + 50);
+    const end = Math.min(lines.length, endLine || startLine + excerptLines);
     return lines.slice(start, end).join('\n');
   } catch (e) {
     debug(`readSourceRange failed for ${file}: ${e.message}`);
@@ -28,12 +29,15 @@ export function readSourceRange(repoRoot, file, startLine, endLine) {
   }
 }
 
-export function extractSummary(fileLines, line) {
+export function extractSummary(fileLines, line, opts = {}) {
   if (!fileLines || !line || line <= 1) return null;
   const idx = line - 2; // line above the definition (0-indexed)
-  // Scan up to 10 lines above for JSDoc or comment
+  const jsdocEndScanLines = opts.jsdocEndScanLines ?? 10;
+  const jsdocOpenScanLines = opts.jsdocOpenScanLines ?? 20;
+  const summaryMaxChars = opts.summaryMaxChars ?? 100;
+  // Scan up for JSDoc or comment
   let jsdocEnd = -1;
-  for (let i = idx; i >= Math.max(0, idx - 10); i--) {
+  for (let i = idx; i >= Math.max(0, idx - jsdocEndScanLines); i--) {
     const trimmed = fileLines[i].trim();
     if (trimmed.endsWith('*/')) {
       jsdocEnd = i;
@@ -45,13 +49,13 @@ export function extractSummary(fileLines, line) {
         .replace(/^\/\/\s*/, '')
         .replace(/^#\s*/, '')
         .trim();
-      return text.length > 100 ? `${text.slice(0, 100)}...` : text;
+      return text.length > summaryMaxChars ? `${text.slice(0, summaryMaxChars)}...` : text;
     }
     if (trimmed !== '' && !trimmed.startsWith('*') && !trimmed.startsWith('/*')) break;
   }
   if (jsdocEnd >= 0) {
     // Find opening /**
-    for (let i = jsdocEnd; i >= Math.max(0, jsdocEnd - 20); i--) {
+    for (let i = jsdocEnd; i >= Math.max(0, jsdocEnd - jsdocOpenScanLines); i--) {
       if (fileLines[i].trim().startsWith('/**')) {
         // Extract first non-tag, non-empty line
         for (let j = i + 1; j <= jsdocEnd; j++) {
@@ -60,7 +64,9 @@ export function extractSummary(fileLines, line) {
             .replace(/^\*\s?/, '')
             .trim();
           if (docLine && !docLine.startsWith('@') && docLine !== '/' && docLine !== '*/') {
-            return docLine.length > 100 ? `${docLine.slice(0, 100)}...` : docLine;
+            return docLine.length > summaryMaxChars
+              ? `${docLine.slice(0, summaryMaxChars)}...`
+              : docLine;
           }
         }
         break;
@@ -70,11 +76,14 @@ export function extractSummary(fileLines, line) {
   return null;
 }
 
-export function extractSignature(fileLines, line) {
+export function extractSignature(fileLines, line, opts = {}) {
   if (!fileLines || !line) return null;
   const idx = line - 1;
-  // Gather up to 5 lines to handle multi-line params
-  const chunk = fileLines.slice(idx, Math.min(fileLines.length, idx + 5)).join('\n');
+  const signatureGatherLines = opts.signatureGatherLines ?? 5;
+  // Gather lines to handle multi-line params
+  const chunk = fileLines
+    .slice(idx, Math.min(fileLines.length, idx + signatureGatherLines))
+    .join('\n');
 
   // JS/TS: function name(params) or (params) => or async function
   let m = chunk.match(
diff --git a/src/shared/paginate.js b/src/shared/paginate.js
index 09cc03b71..e5392a486 100644
--- a/src/shared/paginate.js
+++ b/src/shared/paginate.js
@@ -7,13 +7,11 @@
 
 /** Default limits applied by MCP tool handlers (not by the programmatic API). */
 export const MCP_DEFAULTS = {
-  // Existing
   list_functions: 100,
   query: 10,
   where: 50,
   node_roles: 100,
   export_graph: 500,
-  // Smaller defaults for rich/nested results
   fn_impact: 5,
   context: 5,
   explain: 10,
@@ -33,6 +31,16 @@ export const MCP_DEFAULTS = {
   ast_query: 50,
 };
 
+/**
+ * Get MCP page-size defaults, optionally merged with config overrides.
+ * @param {object} [configDefaults] - Override map from config.mcp.defaults
+ * @returns {object}
+ */
+export function getMcpDefaults(configDefaults) {
+  if (!configDefaults) return MCP_DEFAULTS;
+  return { ...MCP_DEFAULTS, ...configDefaults };
+}
+
 /** Hard cap to prevent abuse via MCP. */
 export const MCP_MAX_LIMIT = 1000;
 
diff --git a/tests/unit/config.test.js b/tests/unit/config.test.js
index 56685830f..d402a4336 100644
--- a/tests/unit/config.test.js
+++ b/tests/unit/config.test.js
@@ -11,6 +11,7 @@ import {
   CONFIG_FILES,
   DEFAULTS,
   loadConfig,
+  mergeConfig,
   resolveSecrets,
 } from '../../src/infrastructure/config.js';
 
@@ -69,12 +70,67 @@ describe('DEFAULTS', () => {
   });
 
   it('has search defaults', () => {
-    expect(DEFAULTS.search).toEqual({ defaultMinScore: 0.2, rrfK: 60, topK: 15 });
+    expect(DEFAULTS.search).toEqual({
+      defaultMinScore: 0.2,
+      rrfK: 60,
+      topK: 15,
+      similarityWarnThreshold: 0.85,
+    });
   });
 
   it('has ci defaults', () => {
     expect(DEFAULTS.ci).toEqual({ failOnCycles: false, impactThreshold: null });
   });
+
+  it('has analysis defaults', () => {
+    expect(DEFAULTS.analysis).toEqual({
+      impactDepth: 3,
+      fnImpactDepth: 5,
+      auditDepth: 3,
+      sequenceDepth: 10,
+      falsePositiveCallers: 20,
+      briefCallerDepth: 5,
+      briefImporterDepth: 5,
+      briefHighRiskCallers: 10,
+      briefMediumRiskCallers: 3,
+    });
+  });
+
+  it('has risk defaults', () => {
+    expect(DEFAULTS.risk.weights).toEqual({
+      fanIn: 0.25,
+      complexity: 0.3,
+      churn: 0.2,
+      role: 0.15,
+      mi: 0.1,
+    });
+    expect(DEFAULTS.risk.defaultRoleWeight).toBe(0.5);
+    expect(DEFAULTS.risk.roleWeights.core).toBe(1.0);
+  });
+
+  it('has display defaults', () => {
+    expect(DEFAULTS.display).toEqual({
+      maxColWidth: 40,
+      excerptLines: 50,
+      summaryMaxChars: 100,
+      jsdocEndScanLines: 10,
+      jsdocOpenScanLines: 20,
+      signatureGatherLines: 5,
+    });
+  });
+
+  it('has community defaults', () => {
+    expect(DEFAULTS.community).toEqual({ resolution: 1.0 });
+  });
+
+  it('has structure defaults', () => {
+    expect(DEFAULTS.structure).toEqual({ cohesionThreshold: 0.3 });
+  });
+
+  it('has mcp defaults', () => {
+    expect(DEFAULTS.mcp.defaults.list_functions).toBe(100);
+    expect(DEFAULTS.mcp.defaults.fn_impact).toBe(5);
+  });
 });
 
 describe('loadConfig', () => {
@@ -160,6 +216,72 @@ describe('loadConfig', () => {
     expect(config.search.defaultMinScore).toBe(0.2);
     expect(config.search.rrfK).toBe(60);
   });
+
+  it('deep-merges nested objects recursively (2+ levels)', () => {
+    const dir = fs.mkdtempSync(path.join(tmpDir, 'deep-merge-'));
+    fs.writeFileSync(
+      path.join(dir, '.codegraphrc.json'),
+      JSON.stringify({ risk: { weights: { complexity: 0.4, churn: 0.1 } } }),
+    );
+    const config = loadConfig(dir);
+    // User overrides applied
+    expect(config.risk.weights.complexity).toBe(0.4);
+    expect(config.risk.weights.churn).toBe(0.1);
+    // Sibling keys preserved (not dropped)
+    expect(config.risk.weights.fanIn).toBe(0.25);
+    expect(config.risk.weights.role).toBe(0.15);
+    expect(config.risk.weights.mi).toBe(0.1);
+    // Sibling sections preserved
+    expect(config.risk.defaultRoleWeight).toBe(0.5);
+    expect(config.risk.roleWeights.core).toBe(1.0);
+  });
+
+  it('loads analysis overrides from config', () => {
+    const dir = fs.mkdtempSync(path.join(tmpDir, 'analysis-'));
+    fs.writeFileSync(
+      path.join(dir, '.codegraphrc.json'),
+      JSON.stringify({ analysis: { fnImpactDepth: 8, falsePositiveCallers: 30 } }),
+    );
+    const config = loadConfig(dir);
+    expect(config.analysis.fnImpactDepth).toBe(8);
+    expect(config.analysis.falsePositiveCallers).toBe(30);
+    // Defaults preserved
+    expect(config.analysis.impactDepth).toBe(3);
+    expect(config.analysis.auditDepth).toBe(3);
+  });
+});
+
+describe('mergeConfig', () => {
+  it('recursively merges nested objects', () => {
+    const defaults = { a: { b: { c: 1, d: 2 }, e: 3 } };
+    const overrides = { a: { b: { c: 10 } } };
+    const result = mergeConfig(defaults, overrides);
+    expect(result.a.b.c).toBe(10);
+    expect(result.a.b.d).toBe(2);
+    expect(result.a.e).toBe(3);
+  });
+
+  it('replaces arrays instead of merging', () => {
+    const defaults = { a: [1, 2, 3] };
+    const overrides = { a: [4] };
+    const result = mergeConfig(defaults, overrides);
+    expect(result.a).toEqual([4]);
+  });
+
+  it('handles overrides with keys not in defaults', () => {
+    const defaults = { a: 1 };
+    const overrides = { b: 2 };
+    const result = mergeConfig(defaults, overrides);
+    expect(result.a).toBe(1);
+    expect(result.b).toBe(2);
+  });
+
+  it('does not mutate defaults', () => {
+    const defaults = { a: { b: 1 } };
+    const overrides = { a: { b: 2 } };
+    mergeConfig(defaults, overrides);
+    expect(defaults.a.b).toBe(1);
+  });
 });
 
 describe('excludeTests hoisting', () => {