diff --git a/src/cli.js b/src/cli.js
index 41f14272..c6d72cf7 100644
--- a/src/cli.js
+++ b/src/cli.js
@@ -16,6 +16,7 @@ import {
 } from './embedder.js';
 import { exportDOT, exportJSON, exportMermaid } from './export.js';
 import { setVerbose } from './logger.js';
+import { printNdjson } from './paginate.js';
 import {
   ALL_SYMBOL_KINDS,
   context,
@@ -127,8 +128,17 @@ program
   .option('-T, --no-tests', 'Exclude test/spec files from results')
   .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
   .option('-j, --json', 'Output as JSON')
+  .option('--limit <number>', 'Max results to return')
+  .option('--offset <number>', 'Skip N results (default: 0)')
+  .option('--ndjson', 'Newline-delimited JSON output')
   .action((file, opts) => {
-    impactAnalysis(file, opts.db, { noTests: resolveNoTests(opts), json: opts.json });
+    impactAnalysis(file, opts.db, {
+      noTests: resolveNoTests(opts),
+      json: opts.json,
+      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
+      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
+      ndjson: opts.ndjson,
+    });
   });
 
 program
@@ -164,8 +174,17 @@ program
   .option('-T, --no-tests', 'Exclude test/spec files from results')
   .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
   .option('-j, --json', 'Output as JSON')
+  .option('--limit <number>', 'Max results to return')
+  .option('--offset <number>', 'Skip N results (default: 0)')
+  .option('--ndjson', 'Newline-delimited JSON output')
   .action((file, opts) => {
-    fileDeps(file, opts.db, { noTests: resolveNoTests(opts), json: opts.json });
+    fileDeps(file, opts.db, {
+      noTests: resolveNoTests(opts),
+      json: opts.json,
+      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
+      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
+      ndjson: opts.ndjson,
+    });
   });
 
 program
@@ -178,6 +197,9 @@ program
   .option('-T, --no-tests', 'Exclude test/spec files from results')
   .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
   .option('-j, --json', 'Output as JSON')
+  .option('--limit <number>', 'Max results to return')
+  .option('--offset <number>', 'Skip N results (default: 0)')
+  .option('--ndjson', 'Newline-delimited JSON output')
   .action((name, opts) => {
     if (opts.kind && !ALL_SYMBOL_KINDS.includes(opts.kind)) {
       console.error(`Invalid kind "${opts.kind}". Valid: ${ALL_SYMBOL_KINDS.join(', ')}`);
@@ -189,6 +211,9 @@ program
       kind: opts.kind,
       noTests: resolveNoTests(opts),
       json: opts.json,
+      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
+      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
+      ndjson: opts.ndjson,
     });
   });
 
@@ -202,6 +227,9 @@ program
   .option('-T, --no-tests', 'Exclude test/spec files from results')
   .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
   .option('-j, --json', 'Output as JSON')
+  .option('--limit <number>', 'Max results to return')
+  .option('--offset <number>', 'Skip N results (default: 0)')
+  .option('--ndjson', 'Newline-delimited JSON output')
   .action((name, opts) => {
     if (opts.kind && !ALL_SYMBOL_KINDS.includes(opts.kind)) {
       console.error(`Invalid kind "${opts.kind}". Valid: ${ALL_SYMBOL_KINDS.join(', ')}`);
@@ -213,6 +241,9 @@ program
       kind: opts.kind,
       noTests: resolveNoTests(opts),
       json: opts.json,
+      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
+      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
+      ndjson: opts.ndjson,
     });
   });
 
@@ -258,6 +289,9 @@ program
   .option('-T, --no-tests', 'Exclude test/spec files from results')
   .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
   .option('-j, --json', 'Output as JSON')
+  .option('--limit <number>', 'Max results to return')
+  .option('--offset <number>', 'Skip N results (default: 0)')
+  .option('--ndjson', 'Newline-delimited JSON output')
   .action((name, opts) => {
     if (opts.kind && !ALL_SYMBOL_KINDS.includes(opts.kind)) {
       console.error(`Invalid kind "${opts.kind}". Valid: ${ALL_SYMBOL_KINDS.join(', ')}`);
@@ -271,6 +305,9 @@ program
       noTests: resolveNoTests(opts),
       includeTests: opts.withTestSource,
       json: opts.json,
+      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
+      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
+      ndjson: opts.ndjson,
     });
   });
 
@@ -282,11 +319,17 @@ program
   .option('-T, --no-tests', 'Exclude test/spec files from results')
   .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
   .option('-j, --json', 'Output as JSON')
+  .option('--limit <number>', 'Max results to return')
+  .option('--offset <number>', 'Skip N results (default: 0)')
+  .option('--ndjson', 'Newline-delimited JSON output')
   .action((target, opts) => {
     explain(target, opts.db, {
       depth: parseInt(opts.depth, 10),
       noTests: resolveNoTests(opts),
       json: opts.json,
+      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
+      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
+      ndjson: opts.ndjson,
     });
   });
 
@@ -327,6 +370,9 @@ program
   .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
   .option('-j, --json', 'Output as JSON')
   .option('-f, --format <format>', 'Output format: text, mermaid, json', 'text')
+  .option('--limit <number>', 'Max results to return')
+  .option('--offset <number>', 'Skip N results (default: 0)')
+  .option('--ndjson', 'Newline-delimited JSON output')
   .action((ref, opts) => {
     diffImpact(opts.db, {
       ref,
@@ -335,6 +381,9 @@ program
       noTests: resolveNoTests(opts),
       json: opts.json,
       format: opts.format,
+      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
+      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
+      ndjson: opts.ndjson,
     });
   });
 
@@ -640,6 +689,8 @@ program
   .option('--rrf-k <number>', 'RRF k parameter for multi-query ranking', '60')
   .option('--mode <mode>', 'Search mode: hybrid, semantic, keyword (default: hybrid)')
   .option('-j, --json', 'Output as JSON')
+  .option('--offset <number>', 'Skip N results (default: 0)')
+  .option('--ndjson', 'Newline-delimited JSON output')
   .action(async (query, opts) => {
     const validModes = ['hybrid', 'semantic', 'keyword'];
     if (opts.mode && !validModes.includes(opts.mode)) {
@@ -671,6 +722,9 @@ program
   .option('-T, --no-tests', 'Exclude test/spec files')
   .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
   .option('-j, --json', 'Output as JSON')
+  .option('--limit <number>', 'Max results to return')
+  .option('--offset <number>', 'Skip N results (default: 0)')
+  .option('--ndjson', 'Newline-delimited JSON output')
   .action(async (dir, opts) => {
     const { structureData, formatStructure } = await import('./structure.js');
     const data = structureData(opts.db, {
@@ -679,8 +733,12 @@ program
       sort: opts.sort,
       full: opts.full,
       noTests: resolveNoTests(opts),
+      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
+      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
     });
-    if (opts.json) {
+    if (opts.ndjson) {
+      printNdjson(data, 'directories');
+    } else if (opts.json) {
       console.log(JSON.stringify(data, null, 2));
     } else {
       console.log(formatStructure(data));
@@ -699,15 +757,20 @@ program
   .option('-T, --no-tests', 'Exclude test/spec files from results')
   .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
   .option('-j, --json', 'Output as JSON')
+  .option('--offset <number>', 'Skip N results (default: 0)')
+  .option('--ndjson', 'Newline-delimited JSON output')
   .action(async (opts) => {
     const { hotspotsData, formatHotspots } = await import('./structure.js');
     const data = hotspotsData(opts.db, {
       metric: opts.metric,
       level: opts.level,
       limit: parseInt(opts.limit, 10),
+      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
       noTests: resolveNoTests(opts),
     });
-    if (opts.json) {
+    if (opts.ndjson) {
+      printNdjson(data, 'hotspots');
+    } else if (opts.json) {
       console.log(JSON.stringify(data, null, 2));
     } else {
       console.log(formatHotspots(data));
@@ -757,6 +820,8 @@ program
   .option('-T, --no-tests', 'Exclude test/spec files')
   .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
   .option('-j, --json', 'Output as JSON')
+  .option('--offset <number>', 'Skip N results (default: 0)')
+  .option('--ndjson', 'Newline-delimited JSON output')
   .action(async (file, opts) => {
     const { analyzeCoChanges, coChangeData, coChangeTopData, formatCoChange, formatCoChangeTop } =
       await import('./cochange.js');
@@ -783,20 +848,25 @@ program
 
     const queryOpts = {
       limit: parseInt(opts.limit, 10),
+      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
       minJaccard: opts.minJaccard ? parseFloat(opts.minJaccard) : config.coChange?.minJaccard,
       noTests: resolveNoTests(opts),
     };
 
     if (file) {
       const data = coChangeData(file, opts.db, queryOpts);
-      if (opts.json) {
+      if (opts.ndjson) {
+        printNdjson(data, 'partners');
+      } else if (opts.json) {
         console.log(JSON.stringify(data, null, 2));
       } else {
         console.log(formatCoChange(data));
       }
     } else {
       const data = coChangeTopData(opts.db, queryOpts);
-      if (opts.json) {
+      if (opts.ndjson) {
+        printNdjson(data, 'pairs');
+      } else if (opts.json) {
         console.log(JSON.stringify(data, null, 2));
       } else {
         console.log(formatCoChangeTop(data));
@@ -860,6 +930,8 @@ program
   .option('-T, --no-tests', 'Exclude test/spec files from results')
   .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
   .option('-j, --json', 'Output as JSON')
+  .option('--offset <number>', 'Skip N results (default: 0)')
+  .option('--ndjson', 'Newline-delimited JSON output')
   .action(async (target, opts) => {
     if (opts.kind && !ALL_SYMBOL_KINDS.includes(opts.kind)) {
       console.error(`Invalid kind "${opts.kind}". Valid: ${ALL_SYMBOL_KINDS.join(', ')}`);
@@ -869,6 +941,7 @@ program
     complexity(opts.db, {
       target,
       limit: parseInt(opts.limit, 10),
+      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
       sort: opts.sort,
       aboveThreshold: opts.aboveThreshold,
       health: opts.health,
@@ -876,6 +949,7 @@ program
       kind: opts.kind,
       noTests: resolveNoTests(opts),
       json: opts.json,
+      ndjson: opts.ndjson,
     });
   });
 
@@ -888,6 +962,9 @@ program
   .option('-f, --file <path>', 'Scope to file (partial match)')
   .option('-k, --kind <kind>', 'Filter by symbol kind')
   .option('-j, --json', 'Output as JSON')
+  .option('--limit <number>', 'Max results to return')
+  .option('--offset <number>', 'Skip N results (default: 0)')
+  .option('--ndjson', 'Newline-delimited JSON output')
   .action(async (opts) => {
     if (opts.kind && !ALL_SYMBOL_KINDS.includes(opts.kind)) {
       console.error(`Invalid kind "${opts.kind}". Valid: ${ALL_SYMBOL_KINDS.join(', ')}`);
@@ -899,6 +976,9 @@ program
       kind: opts.kind,
       noTests: resolveNoTests(opts),
       json: opts.json,
+      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
+      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
+      ndjson: opts.ndjson,
     });
   });
 
@@ -912,6 +992,9 @@ program
   .option('-T, --no-tests', 'Exclude test/spec files from results')
   .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
   .option('-j, --json', 'Output as JSON')
+  .option('--limit <number>', 'Max results to return')
+  .option('--offset <number>', 'Skip N results (default: 0)')
+  .option('--ndjson', 'Newline-delimited JSON output')
   .action(async (opts) => {
     const { communities } = await import('./communities.js');
     communities(opts.db, {
@@ -920,6 +1003,9 @@ program
       drift: opts.drift,
       noTests: resolveNoTests(opts),
       json: opts.json,
+      limit: opts.limit ? parseInt(opts.limit, 10) : undefined,
+      offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
+      ndjson: opts.ndjson,
     });
   });
 
diff --git a/src/cochange.js b/src/cochange.js
index b08ce8db..d1fb2ed3 100644
--- a/src/cochange.js
+++ b/src/cochange.js
@@ -11,6 +11,7 @@ import path from 'node:path';
 import { normalizePath } from './constants.js';
 import { closeDb, findDbPath, initSchema, openDb, openReadonlyOrFail } from './db.js';
 import { warn } from './logger.js';
+import { paginateResult } from './paginate.js';
 import { isTestFile } from './queries.js';
 
 /**
@@ -313,7 +314,8 @@ export function coChangeData(file, customDbPath, opts = {}) {
   const meta = getCoChangeMeta(db);
   closeDb(db);
 
-  return { file: resolvedFile, partners, meta };
+  const base = { file: resolvedFile, partners, meta };
+  return paginateResult(base, 'partners', { limit: opts.limit, offset: opts.offset });
 }
 
 /**
@@ -365,7 +367,8 @@ export function coChangeTopData(customDbPath, opts = {}) {
   const meta = getCoChangeMeta(db);
   closeDb(db);
 
-  return { pairs, meta };
+  const base = { pairs, meta };
+  return paginateResult(base, 'pairs', { limit: opts.limit, offset: opts.offset });
 }
 
 /**
diff --git a/src/communities.js b/src/communities.js
index 7eba4071..926b611b 100644
--- a/src/communities.js
+++ b/src/communities.js
@@ -2,6 +2,7 @@ import path from 'node:path';
 import Graph from 'graphology';
 import louvain from 'graphology-communities-louvain';
 import { openReadonlyOrFail } from './db.js';
+import { paginateResult, printNdjson } from './paginate.js';
 import { isTestFile } from './queries.js';
 
 // ─── Graph Construction ───────────────────────────────────────────────
@@ -201,7 +202,7 @@ export function communitiesData(customDbPath, opts = {}) {
 
   const driftScore = Math.round(((splitRatio + mergeRatio) / 2) * 100);
 
-  return {
+  const base = {
     communities: opts.drift ? [] : communities,
     modularity: +modularity.toFixed(4),
     drift: { splitCandidates, mergeCandidates },
@@ -212,6 +213,7 @@ export function communitiesData(customDbPath, opts = {}) {
       driftScore,
     },
   };
+  return paginateResult(base, 'communities', { limit: opts.limit, offset: opts.offset });
 }
 
 /**
@@ -238,6 +240,10 @@ export function communitySummaryForStats(customDbPath, opts = {}) {
 export function communities(customDbPath, opts = {}) {
   const data = communitiesData(customDbPath, opts);
 
+  if (opts.ndjson) {
+    printNdjson(data, 'communities');
+    return;
+  }
   if (opts.json) {
     console.log(JSON.stringify(data, null, 2));
     return;
diff --git a/src/complexity.js b/src/complexity.js
index 01ffee18..30bee701 100644
--- a/src/complexity.js
+++ b/src/complexity.js
@@ -3,6 +3,7 @@ import path from 'node:path';
 import { loadConfig } from './config.js';
 import { openReadonlyOrFail } from './db.js';
 import { info } from './logger.js';
+import { paginateResult, printNdjson } from './paginate.js';
 import { LANGUAGE_REGISTRY } from './parser.js';
 import { isTestFile } from './queries.js';
 
@@ -1887,10 +1888,9 @@ export function complexityData(customDbPath, opts = {}) {
        FROM function_complexity fc
        JOIN nodes n ON fc.node_id = n.id
        ${where} ${having}
-       ORDER BY ${orderBy}
-       LIMIT ?`,
+       ORDER BY ${orderBy}`,
       )
-      .all(...params, limit);
+      .all(...params);
   } catch {
     db.close();
     return { functions: [], summary: null, thresholds };
@@ -1980,7 +1980,88 @@ export function complexityData(customDbPath, opts = {}) {
   }
 
   db.close();
-  return { functions, summary, thresholds };
+  const base = { functions, summary, thresholds };
+  return paginateResult(base, 'functions', { limit: opts.limit, offset: opts.offset });
+}
+
+/**
+ * Generator: stream complexity rows one-by-one using .iterate() for memory efficiency.
+ * @param {string} [customDbPath]
+ * @param {object} [opts]
+ * @param {boolean} [opts.noTests]
+ * @param {string} [opts.file]
+ * @param {string} [opts.target]
+ * @param {string} [opts.kind]
+ * @param {string} [opts.sort]
+ * @yields {{ name: string, kind: string, file: string, line: number, cognitive: number, cyclomatic: number, maxNesting: number, loc: number, sloc: number }}
+ */
+export function* iterComplexity(customDbPath, opts = {}) {
+  const db = openReadonlyOrFail(customDbPath);
+  try {
+    const noTests = opts.noTests || false;
+    const sort = opts.sort || 'cognitive';
+
+    let where = "WHERE n.kind IN ('function','method')";
+    const params = [];
+
+    if (noTests) {
+      where += ` AND n.file NOT LIKE '%.test.%'
+         AND n.file NOT LIKE '%.spec.%'
+         AND n.file NOT LIKE '%__test__%'
+         AND n.file NOT LIKE '%__tests__%'
+         AND n.file NOT LIKE '%.stories.%'`;
+    }
+    if (opts.target) {
+      where += ' AND n.name LIKE ?';
+      params.push(`%${opts.target}%`);
+    }
+    if (opts.file) {
+      where += ' AND n.file LIKE ?';
+      params.push(`%${opts.file}%`);
+    }
+    if (opts.kind) {
+      where += ' AND n.kind = ?';
+      params.push(opts.kind);
+    }
+
+    const orderMap = {
+      cognitive: 'fc.cognitive DESC',
+      cyclomatic: 'fc.cyclomatic DESC',
+      nesting: 'fc.max_nesting DESC',
+      mi: 'fc.maintainability_index ASC',
+      volume: 'fc.halstead_volume DESC',
+      effort: 'fc.halstead_effort DESC',
+      bugs: 'fc.halstead_bugs DESC',
+      loc: 'fc.loc DESC',
+    };
+    const orderBy = orderMap[sort] || 'fc.cognitive DESC';
+
+    const stmt = db.prepare(
+      `SELECT n.name, n.kind, n.file, n.line, n.end_line,
+              fc.cognitive, fc.cyclomatic, fc.max_nesting, fc.loc, fc.sloc
+       FROM function_complexity fc
+       JOIN nodes n ON fc.node_id = n.id
+       ${where}
+       ORDER BY ${orderBy}`,
+    );
+    for (const r of stmt.iterate(...params)) {
+      if (noTests && isTestFile(r.file)) continue;
+      yield {
+        name: r.name,
+        kind: r.kind,
+        file: r.file,
+        line: r.line,
+        endLine: r.end_line || null,
+        cognitive: r.cognitive,
+        cyclomatic: r.cyclomatic,
+        maxNesting: r.max_nesting,
+        loc: r.loc || 0,
+        sloc: r.sloc || 0,
+      };
+    }
+  } finally {
+    db.close();
+  }
 }
 
 /**
@@ -1989,6 +2070,10 @@ export function complexityData(customDbPath, opts = {}) {
 export function complexity(customDbPath, opts = {}) {
   const data = complexityData(customDbPath, opts);
 
+  if (opts.ndjson) {
+    printNdjson(data, 'functions');
+    return;
+  }
   if (opts.json) {
     console.log(JSON.stringify(data, null, 2));
     return;
diff --git a/src/flow.js b/src/flow.js
index 93381652..ab59fe45 100644
--- a/src/flow.js
+++ b/src/flow.js
@@ -6,7 +6,7 @@
  */
 
 import { openReadonlyOrFail } from './db.js';
-import { paginateResult } from './paginate.js';
+import { paginateResult, printNdjson } from './paginate.js';
 import { isTestFile, kindIcon } from './queries.js';
 import { FRAMEWORK_ENTRY_PREFIXES } from './structure.js';
 
@@ -204,7 +204,7 @@ export function flowData(name, dbPath, opts = {}) {
   }
 
   db.close();
-  return {
+  const base = {
     entry,
     depth: maxDepth,
     steps,
@@ -213,6 +213,7 @@ export function flowData(name, dbPath, opts = {}) {
     totalReached: visited.size - 1, // exclude the entry node itself
     truncated,
   };
+  return paginateResult(base, 'steps', { limit: opts.limit, offset: opts.offset });
 }
 
 /**
@@ -293,8 +294,7 @@ export function flow(name, dbPath, opts = {}) {
       offset: opts.offset,
     });
     if (opts.ndjson) {
-      if (data._pagination) console.log(JSON.stringify({ _meta: data._pagination }));
-      for (const e of data.entries) console.log(JSON.stringify(e));
+      printNdjson(data, 'entries');
       return;
     }
     if (opts.json) {
diff --git a/src/index.js b/src/index.js
index b195d8c6..c9f5f862 100644
--- a/src/index.js
+++ b/src/index.js
@@ -30,6 +30,7 @@ export {
   computeLOCMetrics,
   computeMaintainabilityIndex,
   HALSTEAD_RULES,
+  iterComplexity,
 } from './complexity.js';
 // Configuration
 export { loadConfig } from './config.js';
@@ -75,7 +76,7 @@ export { isNativeAvailable } from './native.js';
 // Ownership (CODEOWNERS)
 export { matchOwners, owners, ownersData, ownersForFiles, parseCodeowners } from './owners.js';
 // Pagination utilities
-export { MCP_DEFAULTS, MCP_MAX_LIMIT, paginate, paginateResult } from './paginate.js';
+export { MCP_DEFAULTS, MCP_MAX_LIMIT, paginate, paginateResult, printNdjson } from './paginate.js';
 
 // Unified parser API
 export { getActiveEngine, parseFileAuto, parseFilesAuto } from './parser.js';
@@ -92,6 +93,9 @@ export {
   fnDepsData,
   fnImpactData,
   impactAnalysisData,
+  iterListFunctions,
+  iterRoles,
+  iterWhere,
   kindIcon,
   moduleMapData,
   pathData,
diff --git a/src/manifesto.js b/src/manifesto.js
index 8fc907ff..3549860a 100644
--- a/src/manifesto.js
+++ b/src/manifesto.js
@@ -2,6 +2,7 @@ import { loadConfig } from './config.js';
 import { findCycles } from './cycles.js';
 import { openReadonlyOrFail } from './db.js';
 import { debug } from './logger.js';
+import { paginateResult, printNdjson } from './paginate.js';
 
 // ─── Rule Definitions ─────────────────────────────────────────────────
 
@@ -354,12 +355,13 @@ export function manifestoData(customDbPath, opts = {}) {
       violationCount: violations.length,
     };
 
-    return {
+    const base = {
       rules: ruleResults,
       violations,
       summary,
       passed: failViolations.length === 0,
     };
+    return paginateResult(base, 'violations', { limit: opts.limit, offset: opts.offset });
   } finally {
     db.close();
   }
@@ -371,6 +373,11 @@ export function manifestoData(customDbPath, opts = {}) {
 export function manifesto(customDbPath, opts = {}) {
   const data = manifestoData(customDbPath, opts);
 
+  if (opts.ndjson) {
+    printNdjson(data, 'violations');
+    if (!data.passed) process.exit(1);
+    return;
+  }
   if (opts.json) {
     console.log(JSON.stringify(data, null, 2));
     if (!data.passed) process.exit(1);
diff --git a/src/mcp.js b/src/mcp.js
index ee11bb3c..19732931 100644
--- a/src/mcp.js
+++ b/src/mcp.js
@@ -50,6 +50,7 @@ const BASE_TOOLS = [
       properties: {
         file: { type: 'string', description: 'File path (partial match supported)' },
         no_tests: { type: 'boolean', description: 'Exclude test files', default: false },
+        ...PAGINATION_PROPS,
       },
       required: ['file'],
     },
@@ -62,6 +63,7 @@ const BASE_TOOLS = [
       properties: {
         file: { type: 'string', description: 'File path to analyze' },
         no_tests: { type: 'boolean', description: 'Exclude test files', default: false },
+        ...PAGINATION_PROPS,
       },
       required: ['file'],
     },
@@ -103,6 +105,7 @@ const BASE_TOOLS = [
           description: 'Filter to a specific symbol kind',
         },
         no_tests: { type: 'boolean', description: 'Exclude test files', default: false },
+        ...PAGINATION_PROPS,
       },
       required: ['name'],
     },
@@ -126,6 +129,7 @@ const BASE_TOOLS = [
           description: 'Filter to a specific symbol kind',
         },
         no_tests: { type: 'boolean', description: 'Exclude test files', default: false },
+        ...PAGINATION_PROPS,
       },
       required: ['name'],
     },
@@ -190,6 +194,7 @@ const BASE_TOOLS = [
           description: 'Include test file source code',
           default: false,
         },
+        ...PAGINATION_PROPS,
       },
       required: ['name'],
     },
@@ -203,6 +208,7 @@ const BASE_TOOLS = [
       properties: {
         target: { type: 'string', description: 'File path or function name' },
         no_tests: { type: 'boolean', description: 'Exclude test files', default: false },
+        ...PAGINATION_PROPS,
       },
       required: ['target'],
     },
@@ -241,6 +247,7 @@ const BASE_TOOLS = [
           enum: ['json', 'mermaid'],
           description: 'Output format (default: json)',
         },
+        ...PAGINATION_PROPS,
       },
     },
   },
@@ -260,6 +267,7 @@ const BASE_TOOLS = [
           description:
             'Search mode: hybrid (BM25 + semantic, default), semantic (embeddings only), keyword (BM25 only)',
         },
+        ...PAGINATION_PROPS,
       },
       required: ['query'],
     },
@@ -318,6 +326,7 @@ const BASE_TOOLS = [
           description: 'Return all files without limit',
           default: false,
         },
+        ...PAGINATION_PROPS,
       },
     },
   },
@@ -358,6 +367,7 @@ const BASE_TOOLS = [
         },
         limit: { type: 'number', description: 'Number of results to return', default: 10 },
         no_tests: { type: 'boolean', description: 'Exclude test files', default: false },
+        offset: { type: 'number', description: 'Skip this many results (pagination, default: 0)' },
       },
     },
   },
@@ -379,6 +389,7 @@ const BASE_TOOLS = [
           default: 0.3,
         },
         no_tests: { type: 'boolean', description: 'Exclude test files', default: false },
+        offset: { type: 'number', description: 'Skip this many results (pagination, default: 0)' },
       },
     },
   },
@@ -405,6 +416,7 @@ const BASE_TOOLS = [
           description: 'Filter to a specific symbol kind',
         },
         no_tests: { type: 'boolean', description: 'Exclude test files', default: false },
+        ...PAGINATION_PROPS,
       },
       required: ['name'],
     },
@@ -452,6 +464,7 @@ const BASE_TOOLS = [
           type: 'string',
           description: 'Filter by symbol kind (function, method, class, etc.)',
         },
+        offset: { type: 'number', description: 'Skip this many results (pagination, default: 0)' },
       },
     },
   },
@@ -468,6 +481,7 @@ const BASE_TOOLS = [
           type: 'string',
           description: 'Filter by symbol kind (function, method, class, etc.)',
         },
+        ...PAGINATION_PROPS,
       },
     },
   },
@@ -494,6 +508,7 @@ const BASE_TOOLS = [
           default: false,
         },
         no_tests: { type: 'boolean', description: 'Exclude test files', default: false },
+        ...PAGINATION_PROPS,
       },
     },
   },
@@ -671,10 +686,18 @@ export async function startMCPServer(customDbPath, options = {}) {
           });
           break;
         case 'file_deps':
-          result = fileDepsData(args.file, dbPath, { noTests: args.no_tests });
+          result = fileDepsData(args.file, dbPath, {
+            noTests: args.no_tests,
+            limit: Math.min(args.limit ?? MCP_DEFAULTS.file_deps, MCP_MAX_LIMIT),
+            offset: args.offset ?? 0,
+          });
           break;
         case 'impact_analysis':
-          result = impactAnalysisData(args.file, dbPath, { noTests: args.no_tests });
+          result = impactAnalysisData(args.file, dbPath, {
+            noTests: args.no_tests,
+            limit: Math.min(args.limit ?? MCP_DEFAULTS.impact_analysis, MCP_MAX_LIMIT),
+            offset: args.offset ?? 0,
+          });
           break;
         case 'find_cycles': {
           const db = new Database(findDbPath(dbPath), { readonly: true });
@@ -692,6 +715,8 @@ export async function startMCPServer(customDbPath, options = {}) {
             file: args.file,
             kind: args.kind,
             noTests: args.no_tests,
+            limit: Math.min(args.limit ?? MCP_DEFAULTS.fn_deps, MCP_MAX_LIMIT),
+            offset: args.offset ?? 0,
           });
           break;
         case 'fn_impact':
@@ -700,6 +725,8 @@ export async function startMCPServer(customDbPath, options = {}) {
             file: args.file,
             kind: args.kind,
             noTests: args.no_tests,
+            limit: Math.min(args.limit ?? MCP_DEFAULTS.fn_impact, MCP_MAX_LIMIT),
+            offset: args.offset ?? 0,
           });
           break;
         case 'symbol_path':
@@ -721,10 +748,16 @@ export async function startMCPServer(customDbPath, options = {}) {
             noSource: args.no_source,
             noTests: args.no_tests,
             includeTests: args.include_tests,
+            limit: Math.min(args.limit ?? MCP_DEFAULTS.context, MCP_MAX_LIMIT),
+            offset: args.offset ?? 0,
           });
           break;
         case 'explain':
-          result = explainData(args.target, dbPath, { noTests: args.no_tests });
+          result = explainData(args.target, dbPath, {
+            noTests: args.no_tests,
+            limit: Math.min(args.limit ?? MCP_DEFAULTS.explain, MCP_MAX_LIMIT),
+            offset: args.offset ?? 0,
+          });
           break;
         case 'where':
           result = whereData(args.target, dbPath, {
@@ -748,12 +781,18 @@ export async function startMCPServer(customDbPath, options = {}) {
               ref: args.ref,
               depth: args.depth,
               noTests: args.no_tests,
+              limit: Math.min(args.limit ?? MCP_DEFAULTS.diff_impact, MCP_MAX_LIMIT),
+              offset: args.offset ?? 0,
             });
           }
           break;
         case 'semantic_search': {
           const mode = args.mode || 'hybrid';
-          const searchOpts = { limit: args.limit, minScore: args.min_score };
+          const searchOpts = {
+            limit: Math.min(args.limit ?? MCP_DEFAULTS.semantic_search, MCP_MAX_LIMIT),
+            offset: args.offset ?? 0,
+            minScore: args.min_score,
+          };
 
           if (mode === 'keyword') {
             const { ftsSearchData } = await import('./embedder.js');
@@ -864,6 +903,8 @@ export async function startMCPServer(customDbPath, options = {}) {
             depth: args.depth,
             sort: args.sort,
             full: args.full,
+            limit: Math.min(args.limit ?? MCP_DEFAULTS.structure, MCP_MAX_LIMIT),
+            offset: args.offset ?? 0,
           });
           break;
         }
@@ -872,7 +913,8 @@ export async function startMCPServer(customDbPath, options = {}) {
           result = hotspotsData(dbPath, {
             metric: args.metric,
             level: args.level,
-            limit: args.limit,
+            limit: Math.min(args.limit ?? MCP_DEFAULTS.hotspots, MCP_MAX_LIMIT),
+            offset: args.offset ?? 0,
             noTests: args.no_tests,
           });
           break;
@@ -881,12 +923,14 @@ export async function startMCPServer(customDbPath, options = {}) {
           const { coChangeData, coChangeTopData } = await import('./cochange.js');
           result = args.file
             ? coChangeData(args.file, dbPath, {
-                limit: args.limit,
+                limit: Math.min(args.limit ?? MCP_DEFAULTS.co_changes, MCP_MAX_LIMIT),
+                offset: args.offset ?? 0,
                 minJaccard: args.min_jaccard,
                 noTests: args.no_tests,
               })
             : coChangeTopData(dbPath, {
-                limit: args.limit,
+                limit: Math.min(args.limit ?? MCP_DEFAULTS.co_changes, MCP_MAX_LIMIT),
+                offset: args.offset ?? 0,
                 minJaccard: args.min_jaccard,
                 noTests: args.no_tests,
               });
@@ -899,6 +943,8 @@ export async function startMCPServer(customDbPath, options = {}) {
             file: args.file,
             kind: args.kind,
             noTests: args.no_tests,
+            limit: Math.min(args.limit ?? MCP_DEFAULTS.execution_flow, MCP_MAX_LIMIT),
+            offset: args.offset ?? 0,
           });
           break;
         }
@@ -916,7 +962,8 @@ export async function startMCPServer(customDbPath, options = {}) {
           result = complexityData(dbPath, {
             target: args.name,
             file: args.file,
-            limit: args.limit,
+            limit: Math.min(args.limit ?? MCP_DEFAULTS.complexity, MCP_MAX_LIMIT),
+            offset: args.offset ?? 0,
             sort: args.sort,
             aboveThreshold: args.above_threshold,
             health: args.health,
@@ -931,6 +978,8 @@ export async function startMCPServer(customDbPath, options = {}) {
             file: args.file,
             noTests: args.no_tests,
             kind: args.kind,
+            limit: Math.min(args.limit ?? MCP_DEFAULTS.manifesto, MCP_MAX_LIMIT),
+            offset: args.offset ?? 0,
           });
           break;
         }
@@ -941,6 +990,8 @@ export async function startMCPServer(customDbPath, options = {}) {
             resolution: args.resolution,
             drift: args.drift,
             noTests: args.no_tests,
+            limit: Math.min(args.limit ?? MCP_DEFAULTS.communities, MCP_MAX_LIMIT),
+            offset: args.offset ?? 0,
           });
           break;
         }
diff --git a/src/paginate.js b/src/paginate.js
index 7109f0bc..a93ec1da 100644
--- a/src/paginate.js
+++ b/src/paginate.js
@@ -7,12 +7,29 @@
 
 /** Default limits applied by MCP tool handlers (not by the programmatic API). */
 export const MCP_DEFAULTS = {
+  // Existing
   list_functions: 100,
   query_function: 50,
   where: 50,
   node_roles: 100,
   list_entry_points: 100,
   export_graph: 500,
+  // Smaller defaults for rich/nested results
+  fn_deps: 10,
+  fn_impact: 5,
+  context: 5,
+  explain: 10,
+  file_deps: 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,
 };
 
 /** Hard cap to prevent abuse via MCP. */
@@ -68,3 +85,20 @@ export function paginateResult(result, field, { limit, offset } = {}) {
   const { items, pagination } = paginate(arr, { limit, offset });
   return { ...result, [field]: items, _pagination: pagination };
 }
+
+/**
+ * Print data as newline-delimited JSON (NDJSON).
+ *
+ * Emits a `_meta` line with pagination info (if present), then one JSON
+ * line per item in the named array field.
+ *
+ * @param {object} data   - Result object (may contain `_pagination`)
+ * @param {string} field  - Array field name to stream (e.g. `'results'`)
+ */
+export function printNdjson(data, field) {
+  if (data._pagination) console.log(JSON.stringify({ _meta: data._pagination }));
+  const items = data[field];
+  if (Array.isArray(items)) {
+    for (const item of items) console.log(JSON.stringify(item));
+  }
+}
diff --git a/src/queries.js b/src/queries.js
index 9b1929ab..2a8df478 100644
--- a/src/queries.js
+++ b/src/queries.js
@@ -6,7 +6,7 @@ import { findCycles } from './cycles.js';
 import { findDbPath, openReadonlyOrFail } from './db.js';
 import { debug } from './logger.js';
 import { ownersForFiles } from './owners.js';
-import { paginateResult } from './paginate.js';
+import { paginateResult, printNdjson } from './paginate.js';
 import { LANGUAGE_REGISTRY } from './parser.js';
 
 /**
@@ -392,7 +392,8 @@ export function fileDepsData(file, customDbPath, opts = {}) {
   });
 
   db.close();
-  return { file, results };
+  const base = { file, results };
+  return paginateResult(base, 'results', { limit: opts.limit, offset: opts.offset });
 }
 
 export function fnDepsData(name, customDbPath, opts = {}) {
@@ -512,7 +513,8 @@ export function fnDepsData(name, customDbPath, opts = {}) {
   });
 
   db.close();
-  return { name, results };
+  const base = { name, results };
+  return paginateResult(base, 'results', { limit: opts.limit, offset: opts.offset });
 }
 
 export function fnImpactData(name, customDbPath, opts = {}) {
@@ -526,7 +528,7 @@ export function fnImpactData(name, customDbPath, opts = {}) {
     return { name, results: [] };
   }
 
-  const results = nodes.slice(0, 3).map((node) => {
+  const results = nodes.map((node) => {
     const visited = new Set([node.id]);
     const levels = {};
     let frontier = [node.id];
@@ -565,7 +567,8 @@ export function fnImpactData(name, customDbPath, opts = {}) {
   });
 
   db.close();
-  return { name, results };
+  const base = { name, results };
+  return paginateResult(base, 'results', { limit: opts.limit, offset: opts.offset });
 }
 
 export function pathData(from, to, customDbPath, opts = {}) {
@@ -1016,7 +1019,7 @@ export function diffImpactData(customDbPath, opts = {}) {
   }
 
   db.close();
-  return {
+  const base = {
     changedFiles: changedRanges.size,
     newFiles: [...newFiles],
     affectedFunctions: functionResults,
@@ -1031,6 +1034,7 @@ export function diffImpactData(customDbPath, opts = {}) {
       ownersAffected: ownership ? ownership.affectedOwners.length : 0,
     },
   };
+  return paginateResult(base, 'affectedFunctions', { limit: opts.limit, offset: opts.offset });
 }
 
 export function diffImpactMermaid(customDbPath, opts = {}) {
@@ -1178,6 +1182,131 @@ export function listFunctionsData(customDbPath, opts = {}) {
   return paginateResult(base, 'functions', { limit: opts.limit, offset: opts.offset });
 }
 
+/**
+ * Generator: stream functions one-by-one using .iterate() for memory efficiency.
+ * @param {string} [customDbPath]
+ * @param {object} [opts]
+ * @param {boolean} [opts.noTests]
+ * @param {string} [opts.file]
+ * @param {string} [opts.pattern]
+ * @yields {{ name: string, kind: string, file: string, line: number, role: string|null }}
+ */
+export function* iterListFunctions(customDbPath, opts = {}) {
+  const db = openReadonlyOrFail(customDbPath);
+  try {
+    const noTests = opts.noTests || false;
+    const kinds = ['function', 'method', 'class'];
+    const placeholders = kinds.map(() => '?').join(', ');
+
+    const conditions = [`kind IN (${placeholders})`];
+    const params = [...kinds];
+
+    if (opts.file) {
+      conditions.push('file LIKE ?');
+      params.push(`%${opts.file}%`);
+    }
+    if (opts.pattern) {
+      conditions.push('name LIKE ?');
+      params.push(`%${opts.pattern}%`);
+    }
+
+    const stmt = db.prepare(
+      `SELECT name, kind, file, line, role FROM nodes WHERE ${conditions.join(' AND ')} ORDER BY file, line`,
+    );
+    for (const row of stmt.iterate(...params)) {
+      if (noTests && isTestFile(row.file)) continue;
+      yield { name: row.name, kind: row.kind, file: row.file, line: row.line, role: row.role };
+    }
+  } finally {
+    db.close();
+  }
+}
+
+/**
+ * Generator: stream role-classified symbols one-by-one.
+ * @param {string} [customDbPath]
+ * @param {object} [opts]
+ * @param {boolean} [opts.noTests]
+ * @param {string} [opts.role]
+ * @param {string} [opts.file]
+ * @yields {{ name: string, kind: string, file: string, line: number, role: string }}
+ */
+export function* iterRoles(customDbPath, opts = {}) {
+  const db = openReadonlyOrFail(customDbPath);
+  try {
+    const noTests = opts.noTests || false;
+    const conditions = ['role IS NOT NULL'];
+    const params = [];
+
+    if (opts.role) {
+      conditions.push('role = ?');
+      params.push(opts.role);
+    }
+    if (opts.file) {
+      conditions.push('file LIKE ?');
+      params.push(`%${opts.file}%`);
+    }
+
+    const stmt = db.prepare(
+      `SELECT name, kind, file, line, role FROM nodes WHERE ${conditions.join(' AND ')} ORDER BY role, file, line`,
+    );
+    for (const row of stmt.iterate(...params)) {
+      if (noTests && isTestFile(row.file)) continue;
+      yield { name: row.name, kind: row.kind, file: row.file, line: row.line, role: row.role };
+    }
+  } finally {
+    db.close();
+  }
+}
+
+/**
+ * Generator: stream symbol lookup results one-by-one.
+ * @param {string} target - Symbol name to search for (partial match)
+ * @param {string} [customDbPath]
+ * @param {object} [opts]
+ * @param {boolean} [opts.noTests]
+ * @yields {{ name: string, kind: string, file: string, line: number, role: string|null, exported: boolean, uses: object[] }}
+ */
+export function* iterWhere(target, customDbPath, opts = {}) {
+  const db = openReadonlyOrFail(customDbPath);
+  try {
+    const noTests = opts.noTests || false;
+    const placeholders = ALL_SYMBOL_KINDS.map(() => '?').join(', ');
+    const stmt = db.prepare(
+      `SELECT * FROM nodes WHERE name LIKE ? AND kind IN (${placeholders}) ORDER BY file, line`,
+    );
+    const crossFileCallersStmt = db.prepare(
+      `SELECT COUNT(*) as cnt FROM edges e JOIN nodes n ON e.source_id = n.id
+       WHERE e.target_id = ? AND e.kind = 'calls' AND n.file != ?`,
+    );
+    const usesStmt = db.prepare(
+      `SELECT n.name, n.file, n.line FROM edges e JOIN nodes n ON e.source_id = n.id
+       WHERE e.target_id = ? AND e.kind = 'calls'`,
+    );
+    for (const node of stmt.iterate(`%${target}%`, ...ALL_SYMBOL_KINDS)) {
+      if (noTests && isTestFile(node.file)) continue;
+
+      const crossFileCallers = crossFileCallersStmt.get(node.id, node.file);
+      const exported = crossFileCallers.cnt > 0;
+
+      let uses = usesStmt.all(node.id);
+      if (noTests) uses = uses.filter((u) => !isTestFile(u.file));
+
+      yield {
+        name: node.name,
+        kind: node.kind,
+        file: node.file,
+        line: node.line,
+        role: node.role || null,
+        exported,
+        uses: uses.map((u) => ({ name: u.name, file: u.file, line: u.line })),
+      };
+    }
+  } finally {
+    db.close();
+  }
+}
+
 export function statsData(customDbPath, opts = {}) {
   const db = openReadonlyOrFail(customDbPath);
   const noTests = opts.noTests || false;
@@ -1572,8 +1701,7 @@ export function queryName(name, customDbPath, opts = {}) {
     offset: opts.offset,
   });
   if (opts.ndjson) {
-    if (data._pagination) console.log(JSON.stringify({ _meta: data._pagination }));
-    for (const r of data.results) console.log(JSON.stringify(r));
+    printNdjson(data, 'results');
     return;
   }
   if (opts.json) {
@@ -1605,7 +1733,11 @@ export function queryName(name, customDbPath, opts = {}) {
 }
 
 export function impactAnalysis(file, customDbPath, opts = {}) {
-  const data = impactAnalysisData(file, customDbPath, { noTests: opts.noTests });
+  const data = impactAnalysisData(file, customDbPath, opts);
+  if (opts.ndjson) {
+    printNdjson(data, 'sources');
+    return;
+  }
   if (opts.json) {
     console.log(JSON.stringify(data, null, 2));
     return;
@@ -1664,7 +1796,11 @@ export function moduleMap(customDbPath, limit = 20, opts = {}) {
 }
 
 export function fileDeps(file, customDbPath, opts = {}) {
-  const data = fileDepsData(file, customDbPath, { noTests: opts.noTests });
+  const data = fileDepsData(file, customDbPath, opts);
+  if (opts.ndjson) {
+    printNdjson(data, 'results');
+    return;
+  }
   if (opts.json) {
     console.log(JSON.stringify(data, null, 2));
     return;
@@ -1695,6 +1831,10 @@ export function fileDeps(file, customDbPath, opts = {}) {
 
 export function fnDeps(name, customDbPath, opts = {}) {
   const data = fnDepsData(name, customDbPath, opts);
+  if (opts.ndjson) {
+    printNdjson(data, 'results');
+    return;
+  }
   if (opts.json) {
     console.log(JSON.stringify(data, null, 2));
     return;
@@ -1863,8 +2003,7 @@ export function contextData(name, customDbPath, opts = {}) {
     return { name, results: [] };
   }
 
-  // Limit to first 5 results
-  nodes = nodes.slice(0, 5);
+  // No hardcoded slice — pagination handles bounding via limit/offset
 
   // File-lines cache to avoid re-reading the same file
   const fileCache = new Map();
@@ -2069,11 +2208,16 @@ export function contextData(name, customDbPath, opts = {}) {
   });
 
   db.close();
-  return { name, results };
+  const base = { name, results };
+  return paginateResult(base, 'results', { limit: opts.limit, offset: opts.offset });
 }
 
 export function context(name, customDbPath, opts = {}) {
   const data = contextData(name, customDbPath, opts);
+  if (opts.ndjson) {
+    printNdjson(data, 'results');
+    return;
+  }
   if (opts.json) {
     console.log(JSON.stringify(data, null, 2));
     return;
@@ -2429,11 +2573,16 @@ export function explainData(target, customDbPath, opts = {}) {
   }
 
   db.close();
-  return { target, kind, results };
+  const base = { target, kind, results };
+  return paginateResult(base, 'results', { limit: opts.limit, offset: opts.offset });
 }
 
 export function explain(target, customDbPath, opts = {}) {
   const data = explainData(target, customDbPath, opts);
+  if (opts.ndjson) {
+    printNdjson(data, 'results');
+    return;
+  }
   if (opts.json) {
     console.log(JSON.stringify(data, null, 2));
     return;
@@ -2664,8 +2813,7 @@ export function whereData(target, customDbPath, opts = {}) {
 export function where(target, customDbPath, opts = {}) {
   const data = whereData(target, customDbPath, opts);
   if (opts.ndjson) {
-    if (data._pagination) console.log(JSON.stringify({ _meta: data._pagination }));
-    for (const r of data.results) console.log(JSON.stringify(r));
+    printNdjson(data, 'results');
     return;
   }
   if (opts.json) {
@@ -2756,8 +2904,7 @@ export function rolesData(customDbPath, opts = {}) {
 export function roles(customDbPath, opts = {}) {
   const data = rolesData(customDbPath, opts);
   if (opts.ndjson) {
-    if (data._pagination) console.log(JSON.stringify({ _meta: data._pagination }));
-    for (const s of data.symbols) console.log(JSON.stringify(s));
+    printNdjson(data, 'symbols');
     return;
   }
   if (opts.json) {
@@ -2798,6 +2945,10 @@ export function roles(customDbPath, opts = {}) {
 
 export function fnImpact(name, customDbPath, opts = {}) {
   const data = fnImpactData(name, customDbPath, opts);
+  if (opts.ndjson) {
+    printNdjson(data, 'results');
+    return;
+  }
   if (opts.json) {
     console.log(JSON.stringify(data, null, 2));
     return;
@@ -2830,6 +2981,10 @@ export function diffImpact(customDbPath, opts = {}) {
     return;
   }
   const data = diffImpactData(customDbPath, opts);
+  if (opts.ndjson) {
+    printNdjson(data, 'affectedFunctions');
+    return;
+  }
   if (opts.json || opts.format === 'json') {
     console.log(JSON.stringify(data, null, 2));
     return;
diff --git a/src/structure.js b/src/structure.js
index ca92ed51..a4c28f41 100644
--- a/src/structure.js
+++ b/src/structure.js
@@ -2,6 +2,7 @@ import path from 'node:path';
 import { normalizePath } from './constants.js';
 import { openReadonlyOrFail } from './db.js';
 import { debug } from './logger.js';
+import { paginateResult } from './paginate.js';
 import { isTestFile } from './queries.js';
 
 // ─── Build-time: insert directory nodes, contains edges, and metrics ────
@@ -463,7 +464,8 @@ export function structureData(customDbPath, opts = {}) {
     }
   }
 
-  return { directories: result, count: result.length };
+  const base = { directories: result, count: result.length };
+  return paginateResult(base, 'directories', { limit: opts.limit, offset: opts.offset });
 }
 
 /**
@@ -534,7 +536,8 @@ export function hotspotsData(customDbPath, opts = {}) {
   }));
 
   db.close();
-  return { metric, level, limit, hotspots };
+  const base = { metric, level, limit, hotspots };
+  return paginateResult(base, 'hotspots', { limit: opts.limit, offset: opts.offset });
 }
 
 /**
diff --git a/tests/integration/context.test.js b/tests/integration/context.test.js
index 39070576..fd2779a7 100644
--- a/tests/integration/context.test.js
+++ b/tests/integration/context.test.js
@@ -229,10 +229,18 @@ describe('contextData', () => {
     expect(pfResult).toBeDefined();
   });
 
-  test('limits results to 5', () => {
-    // We only have a few functions, so this mainly checks the cap logic doesn't crash
-    const data = contextData('', dbPath); // empty name matches everything via LIKE '%%'
-    expect(data.results.length).toBeLessThanOrEqual(5);
+  test('limits results with pagination', () => {
+    // Without limit, all matches are returned (no hardcoded cap)
+    const all = contextData('', dbPath); // empty name matches everything via LIKE '%%'
+    expect(all.results.length).toBeGreaterThan(0);
+
+    // With limit, results are capped and pagination metadata is present
+    const data = contextData('', dbPath, { limit: 2, offset: 0 });
+    expect(data.results.length).toBeLessThanOrEqual(2);
+    if (all.results.length > 2) {
+      expect(data._pagination).toBeDefined();
+      expect(data._pagination.hasMore).toBe(true);
+    }
   });
 
   test('includeTests includes test source', () => {
diff --git a/tests/integration/pagination.test.js b/tests/integration/pagination.test.js
index 4bf652f8..46824881 100644
--- a/tests/integration/pagination.test.js
+++ b/tests/integration/pagination.test.js
@@ -21,8 +21,27 @@ import { afterAll, beforeAll, describe, expect, test } from 'vitest';
 import { initSchema } from '../../src/db.js';
 import { exportDOT, exportJSON, exportMermaid } from '../../src/export.js';
 import { listEntryPointsData } from '../../src/flow.js';
-import { MCP_DEFAULTS, MCP_MAX_LIMIT, paginate, paginateResult } from '../../src/paginate.js';
-import { listFunctionsData, queryNameData, rolesData, whereData } from '../../src/queries.js';
+import {
+  MCP_DEFAULTS,
+  MCP_MAX_LIMIT,
+  paginate,
+  paginateResult,
+  printNdjson,
+} from '../../src/paginate.js';
+import {
+  contextData,
+  explainData,
+  fileDepsData,
+  fnDepsData,
+  fnImpactData,
+  iterListFunctions,
+  iterRoles,
+  iterWhere,
+  listFunctionsData,
+  queryNameData,
+  rolesData,
+  whereData,
+} from '../../src/queries.js';
 
 // ─── Helpers ───────────────────────────────────────────────────────────
 
@@ -297,6 +316,259 @@ describe('listEntryPointsData with pagination', () => {
   });
 });
 
+// ─── fileDepsData with pagination ─────────────────────────────────────
+
+describe('fileDepsData with pagination', () => {
+  test('backward compat: no limit returns all', () => {
+    const data = fileDepsData('a.js', dbPath);
+    expect(data._pagination).toBeUndefined();
+    expect(data.results.length).toBeGreaterThan(0);
+  });
+
+  test('paginated results', () => {
+    const full = fileDepsData('', dbPath);
+    if (full.results.length > 1) {
+      const paginated = fileDepsData('', dbPath, { limit: 1 });
+      expect(paginated.results).toHaveLength(1);
+      expect(paginated._pagination).toBeDefined();
+      expect(paginated._pagination.hasMore).toBe(true);
+    }
+  });
+});
+
+// ─── fnDepsData with pagination ──────────────────────────────────────
+
+describe('fnDepsData with pagination', () => {
+  test('backward compat: no limit returns all', () => {
+    const data = fnDepsData('alpha', dbPath);
+    expect(data._pagination).toBeUndefined();
+    expect(data.results.length).toBeGreaterThan(0);
+  });
+
+  test('paginated results', () => {
+    const full = fnDepsData('a', dbPath);
+    if (full.results.length > 1) {
+      const paginated = fnDepsData('a', dbPath, { limit: 1 });
+      expect(paginated.results).toHaveLength(1);
+      expect(paginated._pagination).toBeDefined();
+      expect(paginated._pagination.hasMore).toBe(true);
+    }
+  });
+});
+
+// ─── fnImpactData with pagination ────────────────────────────────────
+
+describe('fnImpactData with pagination', () => {
+  test('backward compat: no limit returns all', () => {
+    const data = fnImpactData('alpha', dbPath);
+    expect(data._pagination).toBeUndefined();
+    expect(data.results.length).toBeGreaterThan(0);
+  });
+
+  test('paginated results', () => {
+    const full = fnImpactData('a', dbPath);
+    if (full.results.length > 1) {
+      const paginated = fnImpactData('a', dbPath, { limit: 1 });
+      expect(paginated.results).toHaveLength(1);
+      expect(paginated._pagination).toBeDefined();
+    }
+  });
+});
+
+// ─── contextData with pagination ─────────────────────────────────────
+
+describe('contextData with pagination', () => {
+  test('backward compat: no limit returns all', () => {
+    const data = contextData('alpha', dbPath);
+    expect(data._pagination).toBeUndefined();
+    expect(data.results.length).toBeGreaterThan(0);
+  });
+
+  test('paginated results', () => {
+    const full = contextData('a', dbPath);
+    if (full.results.length > 1) {
+      const paginated = contextData('a', dbPath, { limit: 1 });
+      expect(paginated.results).toHaveLength(1);
+      expect(paginated._pagination).toBeDefined();
+    }
+  });
+});
+
+// ─── explainData with pagination ─────────────────────────────────────
+
+describe('explainData with pagination', () => {
+  test('backward compat: no limit returns all', () => {
+    const data = explainData('a.js', dbPath);
+    expect(data._pagination).toBeUndefined();
+    expect(data.results.length).toBeGreaterThan(0);
+  });
+
+  test('paginated results', () => {
+    const full = explainData('', dbPath);
+    if (full.results.length > 1) {
+      const paginated = explainData('', dbPath, { limit: 1 });
+      expect(paginated.results).toHaveLength(1);
+      expect(paginated._pagination).toBeDefined();
+    }
+  });
+});
+
+// ─── MCP new defaults ────────────────────────────────────────────────
+
+describe('MCP new defaults', () => {
+  test('MCP_DEFAULTS has new pagination keys', () => {
+    expect(MCP_DEFAULTS.fn_deps).toBe(10);
+    expect(MCP_DEFAULTS.fn_impact).toBe(5);
+    expect(MCP_DEFAULTS.context).toBe(5);
+    expect(MCP_DEFAULTS.explain).toBe(10);
+    expect(MCP_DEFAULTS.file_deps).toBe(20);
+    expect(MCP_DEFAULTS.diff_impact).toBe(30);
+    expect(MCP_DEFAULTS.semantic_search).toBe(20);
+    expect(MCP_DEFAULTS.execution_flow).toBe(50);
+    expect(MCP_DEFAULTS.hotspots).toBe(20);
+    expect(MCP_DEFAULTS.co_changes).toBe(20);
+    expect(MCP_DEFAULTS.complexity).toBe(30);
+    expect(MCP_DEFAULTS.manifesto).toBe(50);
+    expect(MCP_DEFAULTS.communities).toBe(20);
+    expect(MCP_DEFAULTS.structure).toBe(30);
+  });
+});
+
+// ─── Iterator/Generator APIs ─────────────────────────────────────────
+
+describe('iterListFunctions', () => {
+  test('yields all functions matching listFunctionsData', () => {
+    const full = listFunctionsData(dbPath);
+    const iter = [...iterListFunctions(dbPath)];
+    expect(iter.length).toBe(full.functions.length);
+    for (const item of iter) {
+      expect(item).toHaveProperty('name');
+      expect(item).toHaveProperty('kind');
+      expect(item).toHaveProperty('file');
+      expect(item).toHaveProperty('line');
+    }
+  });
+
+  test('early break closes DB (no leak)', () => {
+    let count = 0;
+    for (const _item of iterListFunctions(dbPath)) {
+      count++;
+      if (count >= 2) break;
+    }
+    expect(count).toBe(2);
+    // If the DB leaked, subsequent operations would fail
+    const data = listFunctionsData(dbPath);
+    expect(data.functions.length).toBeGreaterThan(0);
+  });
+
+  test('noTests filtering works', () => {
+    const all = [...iterListFunctions(dbPath)];
+    const noTests = [...iterListFunctions(dbPath, { noTests: true })];
+    // Should not include test files (fixture has none, so counts equal)
+    expect(noTests.length).toBeLessThanOrEqual(all.length);
+  });
+});
+
+describe('iterRoles', () => {
+  test('yields all role-classified symbols', () => {
+    const full = rolesData(dbPath);
+    const iter = [...iterRoles(dbPath)];
+    expect(iter.length).toBe(full.count);
+    for (const item of iter) {
+      expect(item.role).toBeTruthy();
+    }
+  });
+
+  test('role filter works', () => {
+    const coreOnly = [...iterRoles(dbPath, { role: 'core' })];
+    for (const item of coreOnly) {
+      expect(item.role).toBe('core');
+    }
+  });
+
+  test('early break closes DB (no leak)', () => {
+    let count = 0;
+    for (const _item of iterRoles(dbPath)) {
+      count++;
+      if (count >= 1) break;
+    }
+    expect(count).toBe(1);
+    const data = rolesData(dbPath);
+    expect(data.count).toBeGreaterThan(0);
+  });
+});
+
+describe('iterWhere', () => {
+  test('yields matching symbols with uses', () => {
+    const iter = [...iterWhere('alpha', dbPath)];
+    expect(iter.length).toBeGreaterThan(0);
+    const alpha = iter.find((r) => r.name === 'alpha');
+    expect(alpha).toBeDefined();
+    expect(alpha).toHaveProperty('exported');
+    expect(alpha).toHaveProperty('uses');
+    expect(Array.isArray(alpha.uses)).toBe(true);
+  });
+
+  test('early break closes DB (no leak)', () => {
+    let count = 0;
+    for (const _item of iterWhere('a', dbPath)) {
+      count++;
+      if (count >= 1) break;
+    }
+    expect(count).toBe(1);
+    const data = whereData('alpha', dbPath);
+    expect(data.results.length).toBeGreaterThan(0);
+  });
+});
+
+// ─── printNdjson utility ─────────────────────────────────────────────
+
+describe('printNdjson', () => {
+  test('outputs JSON lines for array field', () => {
+    const logs = [];
+    const origLog = console.log;
+    console.log = (...args) => logs.push(args.join(' '));
+    try {
+      printNdjson({ items: [{ a: 1 }, { b: 2 }] }, 'items');
+      expect(logs).toHaveLength(2);
+      expect(JSON.parse(logs[0])).toEqual({ a: 1 });
+      expect(JSON.parse(logs[1])).toEqual({ b: 2 });
+    } finally {
+      console.log = origLog;
+    }
+  });
+
+  test('emits _meta when _pagination exists', () => {
+    const logs = [];
+    const origLog = console.log;
+    console.log = (...args) => logs.push(args.join(' '));
+    try {
+      printNdjson(
+        { items: [{ x: 1 }], _pagination: { total: 10, offset: 0, limit: 1, hasMore: true } },
+        'items',
+      );
+      expect(logs).toHaveLength(2);
+      const meta = JSON.parse(logs[0]);
+      expect(meta._meta).toBeDefined();
+      expect(meta._meta.total).toBe(10);
+    } finally {
+      console.log = origLog;
+    }
+  });
+
+  test('handles empty array', () => {
+    const logs = [];
+    const origLog = console.log;
+    console.log = (...args) => logs.push(args.join(' '));
+    try {
+      printNdjson({ items: [] }, 'items');
+      expect(logs).toHaveLength(0);
+    } finally {
+      console.log = origLog;
+    }
+  });
+});
+
 // ─── MCP default limits ──────────────────────────────────────────────
 
 describe('MCP defaults', () => {
diff --git a/tests/unit/mcp.test.js b/tests/unit/mcp.test.js
index 1c082085..3df9d876 100644
--- a/tests/unit/mcp.test.js
+++ b/tests/unit/mcp.test.js
@@ -340,6 +340,8 @@ describe('startMCPServer handler dispatch', () => {
       file: 'src/app.js',
       kind: 'function',
       noTests: true,
+      limit: 10,
+      offset: 0,
     });
 
     vi.doUnmock('@modelcontextprotocol/sdk/server/index.js');
@@ -392,7 +394,11 @@ describe('startMCPServer handler dispatch', () => {
     expect(result.isError).toBeUndefined();
     expect(fnImpactMock).toHaveBeenCalledWith('handleClick', '/tmp/test.db', {
       depth: undefined,
+      file: undefined,
+      kind: undefined,
       noTests: undefined,
+      limit: 5,
+      offset: 0,
     });
 
     vi.doUnmock('@modelcontextprotocol/sdk/server/index.js');
@@ -448,6 +454,8 @@ describe('startMCPServer handler dispatch', () => {
       ref: undefined,
       depth: undefined,
       noTests: undefined,
+      limit: 30,
+      offset: 0,
     });
 
     vi.doUnmock('@modelcontextprotocol/sdk/server/index.js');
@@ -1067,8 +1075,10 @@ describe('startMCPServer handler dispatch', () => {
       target: 'buildGraph',
       file: 'src/builder.js',
       limit: 10,
+      offset: 0,
       sort: 'cyclomatic',
       aboveThreshold: true,
+      health: undefined,
       noTests: true,
       kind: 'function',
     });