diff --git a/src/cli/commands/ast.js b/src/cli/commands/ast.js
index 0ba10575..2fe4182d 100644
--- a/src/cli/commands/ast.js
+++ b/src/cli/commands/ast.js
@@ -1,3 +1,4 @@
+import { collectFile } from '../../db/query-builder.js';
 import { ConfigError } from '../../shared/errors.js';
 
 export const command = {
@@ -6,7 +7,7 @@ export const command = {
   queryOpts: true,
   options: [
     ['-k, --kind <kind>', 'Filter by AST node kind (call, new, string, regex, throw, await)'],
-    ['-f, --file <path>', 'Scope to file (partial match)'],
+    ['-f, --file <path>', 'Scope to file (partial match, repeatable)', collectFile],
   ],
   async execute([pattern], opts, ctx) {
     const { AST_NODE_KINDS, astQuery } = await import('../../ast.js');
diff --git a/src/cli/commands/audit.js b/src/cli/commands/audit.js
index abc6db05..b79f65e3 100644
--- a/src/cli/commands/audit.js
+++ b/src/cli/commands/audit.js
@@ -1,3 +1,4 @@
+import { collectFile } from '../../db/query-builder.js';
 import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
 import { audit } from '../../presentation/audit.js';
 import { explain } from '../../presentation/queries-cli.js';
@@ -10,7 +11,7 @@ export const command = {
     ['-d, --db <path>', 'Path to graph.db'],
     ['--quick', 'Structural summary only (skip impact analysis and health metrics)'],
     ['--depth <n>', 'Impact/explain depth', '3'],
-    ['-f, --file <path>', 'Scope to file (partial match)'],
+    ['-f, --file <path>', 'Scope to file (partial match, repeatable)', collectFile],
     ['-k, --kind <kind>', 'Filter by symbol kind'],
     ['-T, --no-tests', 'Exclude test/spec files from results'],
     ['--include-tests', 'Include test/spec files (overrides excludeTests config)'],
diff --git a/src/cli/commands/batch.js b/src/cli/commands/batch.js
index 0beda9ce..f4cdc403 100644
--- a/src/cli/commands/batch.js
+++ b/src/cli/commands/batch.js
@@ -1,4 +1,5 @@
 import fs from 'node:fs';
+import { collectFile } from '../../db/query-builder.js';
 import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
 import { BATCH_COMMANDS, multiBatchData, splitTargets } from '../../features/batch.js';
 import { batch } from '../../presentation/batch.js';
@@ -12,7 +13,7 @@ export const command = {
     ['--from-file <path>', 'Read targets from file (JSON array or newline-delimited)'],
     ['--stdin', 'Read targets from stdin (JSON array)'],
     ['--depth <n>', 'Traversal depth passed to underlying command'],
-    ['-f, --file <path>', 'Scope to file (partial match)'],
+    ['-f, --file <path>', 'Scope to file (partial match, repeatable)', collectFile],
     ['-k, --kind <kind>', 'Filter by symbol kind'],
     ['-T, --no-tests', 'Exclude test/spec files from results'],
     ['--include-tests', 'Include test/spec files (overrides excludeTests config)'],
diff --git a/src/cli/commands/cfg.js b/src/cli/commands/cfg.js
index 7a2fff03..a85e89ca 100644
--- a/src/cli/commands/cfg.js
+++ b/src/cli/commands/cfg.js
@@ -1,3 +1,4 @@
+import { collectFile } from '../../db/query-builder.js';
 import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
 
 export const command = {
@@ -6,7 +7,7 @@ export const command = {
   queryOpts: true,
   options: [
     ['--format <fmt>', 'Output format: text, dot, mermaid', 'text'],
-    ['-f, --file <path>', 'Scope to file (partial match)'],
+    ['-f, --file <path>', 'Scope to file (partial match, repeatable)', collectFile],
     ['-k, --kind <kind>', 'Filter by symbol kind'],
   ],
   validate([_name], opts) {
diff --git a/src/cli/commands/check.js b/src/cli/commands/check.js
index 501e4aa4..b9bf1fcb 100644
--- a/src/cli/commands/check.js
+++ b/src/cli/commands/check.js
@@ -1,3 +1,4 @@
+import { collectFile } from '../../db/query-builder.js';
 import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
 import { ConfigError } from '../../shared/errors.js';
 import { config } from '../shared/options.js';
@@ -31,7 +32,7 @@ export const command = {
     ['--signatures', 'Assert no function declaration lines were modified'],
     ['--boundaries', 'Assert no cross-owner boundary violations'],
     ['--depth <n>', 'Max BFS depth for blast radius (default: 3)'],
-    ['-f, --file <path>', 'Scope to file (partial match, manifesto mode)'],
+    ['-f, --file <path>', 'Scope to file (partial match, repeatable, manifesto mode)', collectFile],
     ['-k, --kind <kind>', 'Filter by symbol kind (manifesto mode)'],
     ['-T, --no-tests', 'Exclude test/spec files from results'],
     ['--include-tests', 'Include test/spec files (overrides excludeTests config)'],
diff --git a/src/cli/commands/children.js b/src/cli/commands/children.js
index f6b2686c..1a5a3f92 100644
--- a/src/cli/commands/children.js
+++ b/src/cli/commands/children.js
@@ -1,3 +1,4 @@
+import { collectFile } from '../../db/query-builder.js';
 import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
 import { children } from '../../presentation/queries-cli.js';
 
@@ -6,7 +7,11 @@ export const command = {
   description: 'List parameters, properties, and constants of a symbol',
   options: [
     ['-d, --db <path>', 'Path to graph.db'],
-    ['-f, --file <path>', 'Scope search to symbols in this file (partial match)'],
+    [
+      '-f, --file <path>',
+      'Scope search to symbols in this file (partial match, repeatable)',
+      collectFile,
+    ],
     ['-k, --kind <kind>', 'Filter to a specific symbol kind'],
     ['-T, --no-tests', 'Exclude test/spec files from results'],
     ['-j, --json', 'Output as JSON'],
diff --git a/src/cli/commands/complexity.js b/src/cli/commands/complexity.js
index f9a08c01..231cd710 100644
--- a/src/cli/commands/complexity.js
+++ b/src/cli/commands/complexity.js
@@ -1,3 +1,4 @@
+import { collectFile } from '../../db/query-builder.js';
 import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
 
 export const command = {
@@ -13,7 +14,7 @@ export const command = {
     ],
     ['--above-threshold', 'Only functions exceeding warn thresholds'],
     ['--health', 'Show health metrics (Halstead, MI) columns'],
-    ['-f, --file <path>', 'Scope to file (partial match)'],
+    ['-f, --file <path>', 'Scope to file (partial match, repeatable)', collectFile],
     ['-k, --kind <kind>', 'Filter by symbol kind'],
     ['-T, --no-tests', 'Exclude test/spec files from results'],
     ['--include-tests', 'Include test/spec files (overrides excludeTests config)'],
diff --git a/src/cli/commands/context.js b/src/cli/commands/context.js
index 16210f55..91ee0772 100644
--- a/src/cli/commands/context.js
+++ b/src/cli/commands/context.js
@@ -1,3 +1,4 @@
+import { collectFile } from '../../db/query-builder.js';
 import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
 import { context } from '../../presentation/queries-cli.js';
 
@@ -7,7 +8,11 @@ export const command = {
   queryOpts: true,
   options: [
     ['--depth <n>', 'Include callee source up to N levels deep', '0'],
-    ['-f, --file <path>', 'Scope search to functions in this file (partial match)'],
+    [
+      '-f, --file <path>',
+      'Scope search to functions in this file (partial match, repeatable)',
+      collectFile,
+    ],
     ['-k, --kind <kind>', 'Filter to a specific symbol kind'],
     ['--no-source', 'Metadata only (skip source extraction)'],
     ['--with-test-source', 'Include test source code'],
diff --git a/src/cli/commands/dataflow.js b/src/cli/commands/dataflow.js
index 7c22f087..e55be263 100644
--- a/src/cli/commands/dataflow.js
+++ b/src/cli/commands/dataflow.js
@@ -1,3 +1,4 @@
+import { collectFile } from '../../db/query-builder.js';
 import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
 
 export const command = {
@@ -5,7 +6,7 @@ export const command = {
   description: 'Show data flow for a function: parameters, return consumers, mutations',
   queryOpts: true,
   options: [
-    ['-f, --file <path>', 'Scope to file (partial match)'],
+    ['-f, --file <path>', 'Scope to file (partial match, repeatable)', collectFile],
     ['-k, --kind <kind>', 'Filter by symbol kind'],
     ['--impact', 'Show data-dependent blast radius'],
     ['--depth <n>', 'Max traversal depth', '5'],
diff --git a/src/cli/commands/flow.js b/src/cli/commands/flow.js
index b281d302..3e161ead 100644
--- a/src/cli/commands/flow.js
+++ b/src/cli/commands/flow.js
@@ -1,3 +1,4 @@
+import { collectFile } from '../../db/query-builder.js';
 import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
 
 export const command = {
@@ -8,7 +9,7 @@ export const command = {
   options: [
     ['--list', 'List all entry points grouped by type'],
     ['--depth <n>', 'Max forward traversal depth', '10'],
-    ['-f, --file <path>', 'Scope to a specific file (partial match)'],
+    ['-f, --file <path>', 'Scope to a specific file (partial match, repeatable)', collectFile],
     ['-k, --kind <kind>', 'Filter by symbol kind'],
   ],
   validate([name], opts) {
diff --git a/src/cli/commands/fn-impact.js b/src/cli/commands/fn-impact.js
index 7715e031..5d2d5943 100644
--- a/src/cli/commands/fn-impact.js
+++ b/src/cli/commands/fn-impact.js
@@ -1,3 +1,4 @@
+import { collectFile } from '../../db/query-builder.js';
 import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
 import { fnImpact } from '../../presentation/queries-cli.js';
 
@@ -7,7 +8,11 @@ export const command = {
   queryOpts: true,
   options: [
     ['--depth <n>', 'Max transitive depth', '5'],
-    ['-f, --file <path>', 'Scope search to functions in this file (partial match)'],
+    [
+      '-f, --file <path>',
+      'Scope search to functions in this file (partial match, repeatable)',
+      collectFile,
+    ],
     ['-k, --kind <kind>', 'Filter to a specific symbol kind'],
   ],
   validate([_name], opts) {
diff --git a/src/cli/commands/owners.js b/src/cli/commands/owners.js
index fee107fc..359426b3 100644
--- a/src/cli/commands/owners.js
+++ b/src/cli/commands/owners.js
@@ -1,3 +1,5 @@
+import { collectFile } from '../../db/query-builder.js';
+
 export const command = {
   name: 'owners [target]',
   description: 'Show CODEOWNERS mapping for files and functions',
@@ -5,7 +7,7 @@ export const command = {
     ['-d, --db <path>', 'Path to graph.db'],
     ['--owner <owner>', 'Filter to a specific owner'],
     ['--boundary', 'Show cross-owner boundary edges'],
-    ['-f, --file <path>', 'Scope to a specific file'],
+    ['-f, --file <path>', 'Scope to a specific file (repeatable)', collectFile],
     ['-k, --kind <kind>', 'Filter by symbol kind'],
     ['-T, --no-tests', 'Exclude test/spec files'],
     ['--include-tests', 'Include test/spec files (overrides excludeTests config)'],
@@ -16,7 +18,7 @@ export const command = {
     owners(opts.db, {
       owner: opts.owner,
       boundary: opts.boundary,
-      file: opts.file || target,
+      file: opts.file && opts.file.length > 0 ? opts.file : target,
       kind: opts.kind,
       noTests: ctx.resolveNoTests(opts),
       json: opts.json,
diff --git a/src/cli/commands/query.js b/src/cli/commands/query.js
index f23edcf5..beca45dd 100644
--- a/src/cli/commands/query.js
+++ b/src/cli/commands/query.js
@@ -1,3 +1,4 @@
+import { collectFile } from '../../db/query-builder.js';
 import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
 import { fnDeps, symbolPath } from '../../presentation/queries-cli.js';
 
@@ -7,7 +8,11 @@ export const command = {
   queryOpts: true,
   options: [
     ['--depth <n>', 'Transitive caller depth', '3'],
-    ['-f, --file <path>', 'Scope search to functions in this file (partial match)'],
+    [
+      '-f, --file <path>',
+      'Scope search to functions in this file (partial match, repeatable)',
+      collectFile,
+    ],
     ['-k, --kind <kind>', 'Filter to a specific symbol kind'],
     ['--path <to>', 'Path mode: find shortest path to <to>'],
     ['--kinds <kinds>', 'Path mode: comma-separated edge kinds to follow (default: calls)'],
diff --git a/src/cli/commands/roles.js b/src/cli/commands/roles.js
index df756333..8677f022 100644
--- a/src/cli/commands/roles.js
+++ b/src/cli/commands/roles.js
@@ -1,3 +1,4 @@
+import { collectFile } from '../../db/query-builder.js';
 import { VALID_ROLES } from '../../domain/queries.js';
 import { roles } from '../../presentation/queries-cli.js';
 
@@ -7,7 +8,7 @@ export const command = {
   options: [
     ['-d, --db <path>', 'Path to graph.db'],
     ['--role <role>', `Filter by role (${VALID_ROLES.join(', ')})`],
-    ['-f, --file <path>', 'Scope to a specific file (partial match)'],
+    ['-f, --file <path>', 'Scope to a specific file (partial match, repeatable)', collectFile],
     ['-T, --no-tests', 'Exclude test/spec files'],
     ['--include-tests', 'Include test/spec files (overrides excludeTests config)'],
     ['-j, --json', 'Output as JSON'],
diff --git a/src/cli/commands/search.js b/src/cli/commands/search.js
index e8670691..c0cd835b 100644
--- a/src/cli/commands/search.js
+++ b/src/cli/commands/search.js
@@ -1,3 +1,4 @@
+import { collectFile } from '../../db/query-builder.js';
 import { search } from '../../domain/search/index.js';
 
 export const command = {
@@ -11,7 +12,7 @@ export const command = {
     ['--include-tests', 'Include test/spec files (overrides excludeTests config)'],
     ['--min-score <score>', 'Minimum similarity threshold', '0.2'],
     ['-k, --kind <kind>', 'Filter by kind: function, method, class'],
-    ['--file <pattern>', 'Filter by file path pattern'],
+    ['--file <pattern>', 'Filter by file path pattern (repeatable)', collectFile],
     ['--rrf-k <number>', 'RRF k parameter for multi-query ranking', '60'],
     ['--mode <mode>', 'Search mode: hybrid, semantic, keyword (default: hybrid)'],
     ['-j, --json', 'Output as JSON'],
@@ -25,6 +26,11 @@ export const command = {
     }
   },
   async execute([query], opts, ctx) {
+    // --file collects into an array; pass single element unwrapped for single
+    // value, or pass the raw array for multi-file scoping.
+    const fileArr = opts.file || [];
+    const filePattern =
+      fileArr.length === 1 ? fileArr[0] : fileArr.length > 1 ? fileArr : undefined;
     await search(query, opts.db, {
       limit: parseInt(opts.limit, 10),
       offset: opts.offset ? parseInt(opts.offset, 10) : undefined,
@@ -32,7 +38,7 @@ export const command = {
       minScore: parseFloat(opts.minScore),
       model: opts.model,
       kind: opts.kind,
-      filePattern: opts.file,
+      filePattern,
       rrfK: parseInt(opts.rrfK, 10),
       mode: opts.mode,
       json: opts.json,
diff --git a/src/cli/commands/sequence.js b/src/cli/commands/sequence.js
index 6bb1e167..35b8c313 100644
--- a/src/cli/commands/sequence.js
+++ b/src/cli/commands/sequence.js
@@ -1,3 +1,4 @@
+import { collectFile } from '../../db/query-builder.js';
 import { EVERY_SYMBOL_KIND } from '../../domain/queries.js';
 
 export const command = {
@@ -7,7 +8,7 @@ export const command = {
   options: [
     ['--depth <n>', 'Max forward traversal depth', '10'],
     ['--dataflow', 'Annotate with parameter names and return arrows from dataflow table'],
-    ['-f, --file <path>', 'Scope to a specific file (partial match)'],
+    ['-f, --file <path>', 'Scope to a specific file (partial match, repeatable)', collectFile],
     ['-k, --kind <kind>', 'Filter by symbol kind'],
   ],
   validate([_name], opts) {
diff --git a/src/cli/commands/triage.js b/src/cli/commands/triage.js
index 828b5623..3aee8a7e 100644
--- a/src/cli/commands/triage.js
+++ b/src/cli/commands/triage.js
@@ -1,3 +1,4 @@
+import { collectFile } from '../../db/query-builder.js';
 import { EVERY_SYMBOL_KIND, VALID_ROLES } from '../../domain/queries.js';
 import { ConfigError } from '../../shared/errors.js';
 
@@ -53,7 +54,7 @@ export const command = {
     ],
     ['--min-score <score>', 'Only show symbols with risk score >= threshold'],
     ['--role <role>', 'Filter by role (entry, core, utility, adapter, leaf, dead)'],
-    ['-f, --file <path>', 'Scope to a specific file (partial match)'],
+    ['-f, --file <path>', 'Scope to a specific file (partial match, repeatable)', collectFile],
     ['-k, --kind <kind>', 'Filter by symbol kind (function, method, class)'],
     ['-T, --no-tests', 'Exclude test/spec files from results'],
     ['--include-tests', 'Include test/spec files (overrides excludeTests config)'],
diff --git a/src/db/query-builder.js b/src/db/query-builder.js
index 10dd1fca..2d15e8cf 100644
--- a/src/db/query-builder.js
+++ b/src/db/query-builder.js
@@ -72,6 +72,55 @@ export function escapeLike(s) {
   return s.replace(/[%_\\]/g, '\\$&');
 }
 
+/**
+ * Normalize a file filter value (string, string[], or falsy) into a flat array.
+ * Returns an empty array when the input is falsy.
+ * @param {string|string[]|undefined|null} file
+ * @returns {string[]}
+ */
+export function normalizeFileFilter(file) {
+  if (!file) return [];
+  return Array.isArray(file) ? file : [file];
+}
+
+/**
+ * Build a SQL condition + params for a multi-value file LIKE filter.
+ * Returns `{ sql: '', params: [] }` when the filter is empty.
+ *
+ * @param {string|string[]} file - One or more partial file paths
+ * @param {string} [column='file'] - The column name to filter on (e.g. 'n.file', 'a.file')
+ * @returns {{ sql: string, params: string[] }}
+ */
+export function buildFileConditionSQL(file, column = 'file') {
+  validateColumn(column);
+  const files = normalizeFileFilter(file);
+  if (files.length === 0) return { sql: '', params: [] };
+  if (files.length === 1) {
+    return {
+      sql: ` AND ${column} LIKE ? ESCAPE '\\'`,
+      params: [`%${escapeLike(files[0])}%`],
+    };
+  }
+  const clauses = files.map(() => `${column} LIKE ? ESCAPE '\\'`);
+  return {
+    sql: ` AND (${clauses.join(' OR ')})`,
+    params: files.map((f) => `%${escapeLike(f)}%`),
+  };
+}
+
+/**
+ * Commander option accumulator for repeatable `--file` flag.
+ * Use as: `['-f, --file <path>', 'Scope to file (partial match, repeatable)', collectFile]`
+ * @param {string} val - New value from Commander
+ * @param {string[]} acc - Accumulated values (undefined on first call)
+ * @returns {string[]}
+ */
+export function collectFile(val, acc) {
+  acc = acc || [];
+  acc.push(val);
+  return acc;
+}
+
 // ─── Standalone Helpers ──────────────────────────────────────────────
 
 /**
@@ -171,11 +220,18 @@ export class NodeQuery {
     return this;
   }
 
-  /** WHERE n.file LIKE ? (no-op if falsy). Escapes LIKE wildcards in the value. */
+  /** WHERE n.file LIKE ? (no-op if falsy). Accepts a single string or string[]. */
   fileFilter(file) {
-    if (!file) return this;
-    this.#conditions.push("n.file LIKE ? ESCAPE '\\'");
-    this.#params.push(`%${escapeLike(file)}%`);
+    const files = normalizeFileFilter(file);
+    if (files.length === 0) return this;
+    if (files.length === 1) {
+      this.#conditions.push("n.file LIKE ? ESCAPE '\\'");
+      this.#params.push(`%${escapeLike(files[0])}%`);
+    } else {
+      const clauses = files.map(() => "n.file LIKE ? ESCAPE '\\'");
+      this.#conditions.push(`(${clauses.join(' OR ')})`);
+      this.#params.push(...files.map((f) => `%${escapeLike(f)}%`));
+    }
     return this;
   }
 
diff --git a/src/db/repository/in-memory-repository.js b/src/db/repository/in-memory-repository.js
index 57e6592e..1607a27c 100644
--- a/src/db/repository/in-memory-repository.js
+++ b/src/db/repository/in-memory-repository.js
@@ -1,6 +1,6 @@
 import { ConfigError } from '../../shared/errors.js';
 import { CORE_SYMBOL_KINDS, EVERY_SYMBOL_KIND, VALID_ROLES } from '../../shared/kinds.js';
-import { escapeLike } from '../query-builder.js';
+import { escapeLike, normalizeFileFilter } from '../query-builder.js';
 import { Repository } from './base.js';
 
 /**
@@ -27,6 +27,17 @@ function likeToRegex(pattern) {
   return new RegExp(`^${regex}$`, 'i');
 }
 
+/**
+ * Build a filter predicate for file matching.
+ * Accepts string, string[], or falsy. Returns null when no filtering needed.
+ */
+function buildFileFilterFn(file) {
+  const files = normalizeFileFilter(file);
+  if (files.length === 0) return null;
+  const regexes = files.map((f) => likeToRegex(`%${escapeLike(f)}%`));
+  return (filePath) => regexes.some((re) => re.test(filePath));
+}
+
 /**
  * In-memory Repository implementation backed by Maps.
  * No SQLite dependency — suitable for fast unit tests.
@@ -121,9 +132,9 @@ export class InMemoryRepository extends Repository {
     if (opts.kinds) {
       nodes = nodes.filter((n) => opts.kinds.includes(n.kind));
     }
-    if (opts.file) {
-      const fileRe = likeToRegex(`%${escapeLike(opts.file)}%`);
-      nodes = nodes.filter((n) => fileRe.test(n.file));
+    {
+      const fileFn = buildFileFilterFn(opts.file);
+      if (fileFn) nodes = nodes.filter((n) => fileFn(n.file));
     }
 
     // Compute fan-in per node
@@ -197,9 +208,9 @@ export class InMemoryRepository extends Repository {
     if (opts.kind) {
       nodes = nodes.filter((n) => n.kind === opts.kind);
     }
-    if (opts.file) {
-      const fileRe = likeToRegex(`%${escapeLike(opts.file)}%`);
-      nodes = nodes.filter((n) => fileRe.test(n.file));
+    {
+      const fileFn = buildFileFilterFn(opts.file);
+      if (fileFn) nodes = nodes.filter((n) => fileFn(n.file));
     }
 
     return nodes.sort((a, b) => a.file.localeCompare(b.file) || a.line - b.line);
@@ -208,9 +219,9 @@ export class InMemoryRepository extends Repository {
   findNodeByQualifiedName(qualifiedName, opts = {}) {
     let nodes = [...this.#nodes.values()].filter((n) => n.qualified_name === qualifiedName);
 
-    if (opts.file) {
-      const fileRe = likeToRegex(`%${escapeLike(opts.file)}%`);
-      nodes = nodes.filter((n) => fileRe.test(n.file));
+    {
+      const fileFn = buildFileFilterFn(opts.file);
+      if (fileFn) nodes = nodes.filter((n) => fileFn(n.file));
     }
 
     return nodes.sort((a, b) => a.file.localeCompare(b.file) || a.line - b.line);
@@ -248,9 +259,9 @@ export class InMemoryRepository extends Repository {
           !n.file.includes('.stories.'),
       );
     }
-    if (opts.file) {
-      const fileRe = likeToRegex(`%${escapeLike(opts.file)}%`);
-      nodes = nodes.filter((n) => fileRe.test(n.file));
+    {
+      const fileFn = buildFileFilterFn(opts.file);
+      if (fileFn) nodes = nodes.filter((n) => fileFn(n.file));
     }
     if (opts.role) {
       nodes = nodes.filter((n) => n.role === opts.role);
@@ -541,9 +552,9 @@ export class InMemoryRepository extends Repository {
       ['function', 'method', 'class'].includes(n.kind),
     );
 
-    if (opts.file) {
-      const fileRe = likeToRegex(`%${escapeLike(opts.file)}%`);
-      nodes = nodes.filter((n) => fileRe.test(n.file));
+    {
+      const fileFn = buildFileFilterFn(opts.file);
+      if (fileFn) nodes = nodes.filter((n) => fileFn(n.file));
     }
     if (opts.pattern) {
       const patternRe = likeToRegex(`%${escapeLike(opts.pattern)}%`);
diff --git a/src/db/repository/nodes.js b/src/db/repository/nodes.js
index fbe2ddf0..ffcf6297 100644
--- a/src/db/repository/nodes.js
+++ b/src/db/repository/nodes.js
@@ -1,6 +1,6 @@
 import { ConfigError } from '../../shared/errors.js';
 import { EVERY_SYMBOL_KIND, VALID_ROLES } from '../../shared/kinds.js';
-import { escapeLike, NodeQuery } from '../query-builder.js';
+import { buildFileConditionSQL, NodeQuery } from '../query-builder.js';
 import { cachedStmt } from './cached-stmt.js';
 
 // ─── Query-builder based lookups (moved from src/db/repository.js) ─────
@@ -267,10 +267,9 @@ export function findNodesByScope(db, scopeName, opts = {}) {
     sql += ' AND kind = ?';
     params.push(opts.kind);
   }
-  if (opts.file) {
-    sql += " AND file LIKE ? ESCAPE '\\'";
-    params.push(`%${escapeLike(opts.file)}%`);
-  }
+  const fc = buildFileConditionSQL(opts.file, 'file');
+  sql += fc.sql;
+  params.push(...fc.params);
   sql += ' ORDER BY file, line';
   return db.prepare(sql).all(...params);
 }
@@ -286,12 +285,11 @@ export function findNodesByScope(db, scopeName, opts = {}) {
  * @returns {object[]}
  */
 export function findNodeByQualifiedName(db, qualifiedName, opts = {}) {
-  if (opts.file) {
+  const fc = buildFileConditionSQL(opts.file, 'file');
+  if (fc.sql) {
     return db
-      .prepare(
-        "SELECT * FROM nodes WHERE qualified_name = ? AND file LIKE ? ESCAPE '\\' ORDER BY file, line",
-      )
-      .all(qualifiedName, `%${escapeLike(opts.file)}%`);
+      .prepare(`SELECT * FROM nodes WHERE qualified_name = ?${fc.sql} ORDER BY file, line`)
+      .all(qualifiedName, ...fc.params);
   }
   return cachedStmt(
     _findNodeByQualifiedNameStmt,
diff --git a/src/domain/analysis/roles.js b/src/domain/analysis/roles.js
index a54362fd..141a10ed 100644
--- a/src/domain/analysis/roles.js
+++ b/src/domain/analysis/roles.js
@@ -1,4 +1,5 @@
 import { openReadonlyOrFail } from '../../db/index.js';
+import { buildFileConditionSQL } from '../../db/query-builder.js';
 import { isTestFile } from '../../infrastructure/test-filter.js';
 import { normalizeSymbol } from '../../shared/normalize.js';
 import { paginateResult } from '../../shared/paginate.js';
@@ -8,8 +9,6 @@ export function rolesData(customDbPath, opts = {}) {
   try {
     const noTests = opts.noTests || false;
     const filterRole = opts.role || null;
-    const filterFile = opts.file || null;
-
     const conditions = ['role IS NOT NULL'];
     const params = [];
 
@@ -17,9 +16,13 @@ export function rolesData(customDbPath, opts = {}) {
       conditions.push('role = ?');
       params.push(filterRole);
     }
-    if (filterFile) {
-      conditions.push('file LIKE ?');
-      params.push(`%${filterFile}%`);
+    {
+      const fc = buildFileConditionSQL(opts.file, 'file');
+      if (fc.sql) {
+        // Strip leading ' AND ' since we're using conditions array
+        conditions.push(fc.sql.replace(/^ AND /, ''));
+        params.push(...fc.params);
+      }
     }
 
     let rows = db
diff --git a/src/domain/search/search/filters.js b/src/domain/search/search/filters.js
index 465e51e0..47becc3a 100644
--- a/src/domain/search/search/filters.js
+++ b/src/domain/search/search/filters.js
@@ -29,15 +29,19 @@ const TEST_PATTERN = /\.(test|spec)\.|__test__|__tests__|\.stories\./;
  * @param {object} opts
  * @param {string} [opts.filePattern] - Glob pattern (only applied if it contains glob chars)
  * @param {boolean} [opts.noTests] - Exclude test/spec files
- * @param {boolean} [opts.isGlob] - Pre-computed: does filePattern contain glob chars?
  * @returns {Array}
  */
 export function applyFilters(rows, opts = {}) {
   let filtered = rows;
-  const isGlob =
-    opts.isGlob !== undefined ? opts.isGlob : opts.filePattern && /[*?[\]]/.test(opts.filePattern);
-  if (isGlob) {
-    filtered = filtered.filter((row) => globMatch(row.file, opts.filePattern));
+  const fp = opts.filePattern;
+  const fpArr = Array.isArray(fp) ? fp : fp ? [fp] : [];
+  if (fpArr.length > 0) {
+    filtered = filtered.filter((row) =>
+      fpArr.some((p) => {
+        const patternIsGlob = /[*?[\]]/.test(p);
+        return patternIsGlob ? globMatch(row.file, p) : row.file.includes(p);
+      }),
+    );
   }
   if (opts.noTests) {
     filtered = filtered.filter((row) => !TEST_PATTERN.test(row.file));
diff --git a/src/domain/search/search/keyword.js b/src/domain/search/search/keyword.js
index e43c5212..4a4e3ed7 100644
--- a/src/domain/search/search/keyword.js
+++ b/src/domain/search/search/keyword.js
@@ -1,4 +1,5 @@
 import { openReadonlyOrFail } from '../../../db/index.js';
+import { buildFileConditionSQL } from '../../../db/query-builder.js';
 import { normalizeSymbol } from '../../queries.js';
 import { hasFtsIndex, sanitizeFtsQuery } from '../stores/fts5.js';
 import { applyFilters } from './filters.js';
@@ -36,10 +37,16 @@ export function ftsSearchData(query, customDbPath, opts = {}) {
       params.push(opts.kind);
     }
 
-    const isGlob = opts.filePattern && /[*?[\]]/.test(opts.filePattern);
-    if (opts.filePattern && !isGlob) {
-      sql += ' AND n.file LIKE ?';
-      params.push(`%${opts.filePattern}%`);
+    const fp = opts.filePattern;
+    const fpArr = Array.isArray(fp) ? fp : fp ? [fp] : [];
+    const isGlob = fpArr.length > 0 && fpArr.some((p) => /[*?[\]]/.test(p));
+    // For non-glob patterns, push filtering into SQL via buildFileConditionSQL
+    // (handles escapeLike + ESCAPE clause). Glob patterns are handled post-query
+    // by applyFilters.
+    if (fpArr.length > 0 && !isGlob) {
+      const fc = buildFileConditionSQL(fpArr, 'n.file');
+      sql += fc.sql;
+      params.push(...fc.params);
     }
 
     sql += ' ORDER BY rank LIMIT ?';
@@ -53,7 +60,7 @@ export function ftsSearchData(query, customDbPath, opts = {}) {
       return { results: [] };
     }
 
-    rows = applyFilters(rows, { ...opts, isGlob });
+    rows = applyFilters(rows, opts);
 
     const hc = new Map();
     const results = rows.slice(0, limit).map((row) => ({
diff --git a/src/domain/search/search/prepare.js b/src/domain/search/search/prepare.js
index 484584c5..fb1552e4 100644
--- a/src/domain/search/search/prepare.js
+++ b/src/domain/search/search/prepare.js
@@ -1,4 +1,5 @@
 import { openReadonlyOrFail } from '../../../db/index.js';
+import { escapeLike } from '../../../db/query-builder.js';
 import { getEmbeddingCount, getEmbeddingMeta } from '../../../db/repository/embeddings.js';
 import { MODELS } from '../models.js';
 import { applyFilters } from './filters.js';
@@ -35,7 +36,9 @@ export function prepareSearch(customDbPath, opts = {}) {
     }
 
     // Pre-filter: allow filtering by kind or file pattern to reduce search space
-    const isGlob = opts.filePattern && /[*?[\]]/.test(opts.filePattern);
+    const fp = opts.filePattern;
+    const fpArr = Array.isArray(fp) ? fp : fp ? [fp] : [];
+    const isGlob = fpArr.length > 0 && fpArr.some((p) => /[*?[\]]/.test(p));
     let sql = `
     SELECT e.node_id, e.vector, e.text_preview, n.name, n.kind, n.file, n.line, n.end_line, n.role
     FROM embeddings e
@@ -47,16 +50,21 @@ export function prepareSearch(customDbPath, opts = {}) {
       conditions.push('n.kind = ?');
       params.push(opts.kind);
     }
-    if (opts.filePattern && !isGlob) {
-      conditions.push('n.file LIKE ?');
-      params.push(`%${opts.filePattern}%`);
+    if (fpArr.length > 0 && !isGlob) {
+      if (fpArr.length === 1) {
+        conditions.push("n.file LIKE ? ESCAPE '\\'");
+        params.push(`%${escapeLike(fpArr[0])}%`);
+      } else {
+        conditions.push(`(${fpArr.map(() => "n.file LIKE ? ESCAPE '\\'").join(' OR ')})`);
+        params.push(...fpArr.map((f) => `%${escapeLike(f)}%`));
+      }
     }
     if (conditions.length > 0) {
       sql += ` WHERE ${conditions.join(' AND ')}`;
     }
 
     let rows = db.prepare(sql).all(...params);
-    rows = applyFilters(rows, { ...opts, isGlob });
+    rows = applyFilters(rows, opts);
 
     return { db, rows, modelKey, storedDim };
   } catch (err) {
diff --git a/src/features/ast.js b/src/features/ast.js
index 6bc3a371..ad9a6270 100644
--- a/src/features/ast.js
+++ b/src/features/ast.js
@@ -12,6 +12,7 @@ import { buildExtensionSet } from '../ast-analysis/shared.js';
 import { walkWithVisitors } from '../ast-analysis/visitor.js';
 import { createAstStoreVisitor } from '../ast-analysis/visitors/ast-store-visitor.js';
 import { bulkNodeIdsByFile, openReadonlyOrFail } from '../db/index.js';
+import { buildFileConditionSQL } from '../db/query-builder.js';
 import { debug } from '../infrastructure/logger.js';
 import { outputResult } from '../infrastructure/result-formatter.js';
 import { paginateResult } from '../shared/paginate.js';
@@ -193,9 +194,10 @@ export function astQueryData(pattern, customDbPath, opts = {}) {
     params.push(kind);
   }
 
-  if (file) {
-    where += ' AND a.file LIKE ?';
-    params.push(`%${file}%`);
+  {
+    const fc = buildFileConditionSQL(file, 'a.file');
+    where += fc.sql;
+    params.push(...fc.params);
   }
 
   if (noTests) {
diff --git a/src/features/audit.js b/src/features/audit.js
index 7526b2c3..5cc74a6c 100644
--- a/src/features/audit.js
+++ b/src/features/audit.js
@@ -8,6 +8,7 @@
 
 import path from 'node:path';
 import { openReadonlyOrFail } from '../db/index.js';
+import { normalizeFileFilter } from '../db/query-builder.js';
 import { bfsTransitiveCallers } from '../domain/analysis/impact.js';
 import { explainData } from '../domain/queries.js';
 import { loadConfig } from '../infrastructure/config.js';
@@ -100,7 +101,7 @@ function readPhase44(db, nodeId) {
 export function auditData(target, customDbPath, opts = {}) {
   const noTests = opts.noTests || false;
   const maxDepth = opts.depth || 3;
-  const file = opts.file;
+  const fileFilters = normalizeFileFilter(opts.file);
   const kind = opts.kind;
 
   // 1. Get structure via explainData
@@ -109,7 +110,8 @@ export function auditData(target, customDbPath, opts = {}) {
   // Apply --file and --kind filters for function targets
   let results = explained.results;
   if (explained.kind === 'function') {
-    if (file) results = results.filter((r) => r.file.includes(file));
+    if (fileFilters.length > 0)
+      results = results.filter((r) => fileFilters.some((f) => r.file.includes(f)));
     if (kind) results = results.filter((r) => r.kind === kind);
   }
 
diff --git a/src/features/complexity.js b/src/features/complexity.js
index 80a55377..a4a805ec 100644
--- a/src/features/complexity.js
+++ b/src/features/complexity.js
@@ -13,6 +13,7 @@ import {
 import { walkWithVisitors } from '../ast-analysis/visitor.js';
 import { createComplexityVisitor } from '../ast-analysis/visitors/complexity-visitor.js';
 import { getFunctionNodeId, openReadonlyOrFail } from '../db/index.js';
+import { buildFileConditionSQL } from '../db/query-builder.js';
 import { loadConfig } from '../infrastructure/config.js';
 import { debug, info } from '../infrastructure/logger.js';
 import { isTestFile } from '../infrastructure/test-filter.js';
@@ -554,9 +555,10 @@ export function complexityData(customDbPath, opts = {}) {
       where += ' AND n.name LIKE ?';
       params.push(`%${target}%`);
     }
-    if (fileFilter) {
-      where += ' AND n.file LIKE ?';
-      params.push(`%${fileFilter}%`);
+    {
+      const fc = buildFileConditionSQL(fileFilter, 'n.file');
+      where += fc.sql;
+      params.push(...fc.params);
     }
     if (kindFilter) {
       where += ' AND n.kind = ?';
@@ -761,9 +763,10 @@ export function* iterComplexity(customDbPath, opts = {}) {
       where += ' AND n.name LIKE ?';
       params.push(`%${opts.target}%`);
     }
-    if (opts.file) {
-      where += ' AND n.file LIKE ?';
-      params.push(`%${opts.file}%`);
+    {
+      const fc = buildFileConditionSQL(opts.file, 'n.file');
+      where += fc.sql;
+      params.push(...fc.params);
     }
     if (opts.kind) {
       where += ' AND n.kind = ?';
diff --git a/src/features/manifesto.js b/src/features/manifesto.js
index edae49e4..d37fd296 100644
--- a/src/features/manifesto.js
+++ b/src/features/manifesto.js
@@ -1,4 +1,5 @@
 import { openReadonlyOrFail } from '../db/index.js';
+import { buildFileConditionSQL } from '../db/query-builder.js';
 import { findCycles } from '../domain/graph/cycles.js';
 import { loadConfig } from '../infrastructure/config.js';
 import { debug } from '../infrastructure/logger.js';
@@ -144,9 +145,10 @@ function evaluateFunctionRules(db, rules, opts, violations, ruleResults) {
   let where = "WHERE n.kind IN ('function','method')";
   const params = [];
   if (opts.noTests) where += NO_TEST_SQL;
-  if (opts.file) {
-    where += ' AND n.file LIKE ?';
-    params.push(`%${opts.file}%`);
+  {
+    const fc = buildFileConditionSQL(opts.file, 'n.file');
+    where += fc.sql;
+    params.push(...fc.params);
   }
   if (opts.kind) {
     where += ' AND n.kind = ?';
@@ -221,9 +223,10 @@ function evaluateFileRules(db, rules, opts, violations, ruleResults) {
   let where = "WHERE n.kind = 'file'";
   const params = [];
   if (opts.noTests) where += NO_TEST_SQL;
-  if (opts.file) {
-    where += ' AND n.file LIKE ?';
-    params.push(`%${opts.file}%`);
+  {
+    const fc = buildFileConditionSQL(opts.file, 'n.file');
+    where += fc.sql;
+    params.push(...fc.params);
   }
 
   let rows;
diff --git a/src/features/owners.js b/src/features/owners.js
index 58509ff9..3608d947 100644
--- a/src/features/owners.js
+++ b/src/features/owners.js
@@ -1,6 +1,7 @@
 import fs from 'node:fs';
 import path from 'node:path';
 import { findDbPath, openReadonlyOrFail } from '../db/index.js';
+import { normalizeFileFilter } from '../db/query-builder.js';
 import { isTestFile } from '../infrastructure/test-filter.js';
 
 // ─── CODEOWNERS Parsing ──────────────────────────────────────────────
@@ -192,9 +193,9 @@ export function ownersData(customDbPath, opts = {}) {
       .map((r) => r.file);
 
     if (opts.noTests) allFiles = allFiles.filter((f) => !isTestFile(f));
-    if (opts.file) {
-      const filter = opts.file;
-      allFiles = allFiles.filter((f) => f.includes(filter));
+    const fileFilters = normalizeFileFilter(opts.file);
+    if (fileFilters.length > 0) {
+      allFiles = allFiles.filter((f) => fileFilters.some((filter) => f.includes(filter)));
     }
 
     // Map files to owners
diff --git a/src/features/shared/find-nodes.js b/src/features/shared/find-nodes.js
index d888f548..e71b1eac 100644
--- a/src/features/shared/find-nodes.js
+++ b/src/features/shared/find-nodes.js
@@ -1,3 +1,4 @@
+import { buildFileConditionSQL } from '../../db/query-builder.js';
 import { isTestFile } from '../../infrastructure/test-filter.js';
 
 /**
@@ -15,16 +16,13 @@ export function findNodes(db, name, opts = {}, defaultKinds = []) {
   const placeholders = kinds.map(() => '?').join(', ');
   const params = [`%${name}%`, ...kinds];
 
-  let fileCondition = '';
-  if (opts.file) {
-    fileCondition = ' AND file LIKE ?';
-    params.push(`%${opts.file}%`);
-  }
+  const fc = buildFileConditionSQL(opts.file, 'file');
+  params.push(...fc.params);
 
   const rows = db
     .prepare(
       `SELECT * FROM nodes
-       WHERE name LIKE ? AND kind IN (${placeholders})${fileCondition}
+       WHERE name LIKE ? AND kind IN (${placeholders})${fc.sql}
        ORDER BY file, line`,
     )
     .all(...params);
diff --git a/src/shared/generators.js b/src/shared/generators.js
index 3d121f81..75a132ea 100644
--- a/src/shared/generators.js
+++ b/src/shared/generators.js
@@ -1,4 +1,5 @@
 import { iterateFunctionNodes, openReadonlyOrFail } from '../db/index.js';
+import { buildFileConditionSQL } from '../db/query-builder.js';
 import { isTestFile } from '../infrastructure/test-filter.js';
 import { ALL_SYMBOL_KINDS } from './kinds.js';
 
@@ -52,9 +53,12 @@ export function* iterRoles(customDbPath, opts = {}) {
       conditions.push('role = ?');
       params.push(opts.role);
     }
-    if (opts.file) {
-      conditions.push('file LIKE ?');
-      params.push(`%${opts.file}%`);
+    {
+      const fc = buildFileConditionSQL(opts.file, 'file');
+      if (fc.sql) {
+        conditions.push(fc.sql.replace(/^ AND /, ''));
+        params.push(...fc.params);
+      }
     }
 
     const stmt = db.prepare(
diff --git a/tests/unit/query-builder.test.js b/tests/unit/query-builder.test.js
index 7c47285d..a2a15e51 100644
--- a/tests/unit/query-builder.test.js
+++ b/tests/unit/query-builder.test.js
@@ -2,10 +2,13 @@ import Database from 'better-sqlite3';
 import { afterEach, beforeEach, describe, expect, it } from 'vitest';
 import { initSchema } from '../../src/db/migrations.js';
 import {
+  buildFileConditionSQL,
+  collectFile,
   fanInJoinSQL,
   fanOutJoinSQL,
   kindInClause,
   NodeQuery,
+  normalizeFileFilter,
   testFilterSQL,
 } from '../../src/db/query-builder.js';
 
@@ -87,6 +90,71 @@ describe('fanOutJoinSQL', () => {
   });
 });
 
+// ─── normalizeFileFilter ─────────────────────────────────────────────
+
+describe('normalizeFileFilter', () => {
+  it('returns empty array for falsy input', () => {
+    expect(normalizeFileFilter(null)).toEqual([]);
+    expect(normalizeFileFilter(undefined)).toEqual([]);
+    expect(normalizeFileFilter('')).toEqual([]);
+  });
+
+  it('wraps a single string in an array', () => {
+    expect(normalizeFileFilter('foo.js')).toEqual(['foo.js']);
+  });
+
+  it('passes through an array unchanged', () => {
+    expect(normalizeFileFilter(['a.js', 'b.js'])).toEqual(['a.js', 'b.js']);
+  });
+});
+
+// ─── buildFileConditionSQL ──────────────────────────────────────────
+
+describe('buildFileConditionSQL', () => {
+  it('returns empty sql/params for falsy input', () => {
+    expect(buildFileConditionSQL(null)).toEqual({ sql: '', params: [] });
+    expect(buildFileConditionSQL(undefined)).toEqual({ sql: '', params: [] });
+  });
+
+  it('builds single-value LIKE clause', () => {
+    const { sql, params } = buildFileConditionSQL('foo');
+    expect(sql).toContain('LIKE ?');
+    expect(sql).toContain('ESCAPE');
+    expect(params).toEqual(['%foo%']);
+  });
+
+  it('builds multi-value OR clause', () => {
+    const { sql, params } = buildFileConditionSQL(['foo', 'bar']);
+    expect(sql).toContain('OR');
+    expect(sql).toMatch(/LIKE \?.*OR.*LIKE \?/);
+    expect(params).toEqual(['%foo%', '%bar%']);
+  });
+
+  it('uses custom column name', () => {
+    const { sql } = buildFileConditionSQL('foo', 'n.file');
+    expect(sql).toContain('n.file LIKE');
+  });
+
+  it('escapes LIKE wildcards', () => {
+    const { params } = buildFileConditionSQL('file_name%');
+    expect(params[0]).toBe('%file\\_name\\%%');
+  });
+});
+
+// ─── collectFile ────────────────────────────────────────────────────
+
+describe('collectFile', () => {
+  it('creates array on first call', () => {
+    expect(collectFile('a.js', undefined)).toEqual(['a.js']);
+  });
+
+  it('accumulates values on subsequent calls', () => {
+    let acc = collectFile('a.js', undefined);
+    acc = collectFile('b.js', acc);
+    expect(acc).toEqual(['a.js', 'b.js']);
+  });
+});
+
 // ─── NodeQuery ───────────────────────────────────────────────────────
 
 describe('NodeQuery', () => {
@@ -163,6 +231,23 @@ describe('NodeQuery', () => {
     expect(rows.length).toBe(0);
   });
 
+  it('.fileFilter() accepts an array of paths', () => {
+    const rows = new NodeQuery().fileFilter(['foo', 'bar']).all(db);
+    expect(rows.length).toBeGreaterThan(0);
+    expect(rows.every((r) => r.file.includes('foo') || r.file.includes('bar'))).toBe(true);
+    // Should include both foo and bar files
+    const files = new Set(rows.map((r) => r.file));
+    expect(files.has('src/foo.js')).toBe(true);
+    expect(files.has('src/bar.js')).toBe(true);
+  });
+
+  it('.fileFilter() with single-element array works like string', () => {
+    const arrayRows = new NodeQuery().fileFilter(['foo']).all(db);
+    const stringRows = new NodeQuery().fileFilter('foo').all(db);
+    expect(arrayRows.length).toBe(stringRows.length);
+    expect(arrayRows.map((r) => r.name).sort()).toEqual(stringRows.map((r) => r.name).sort());
+  });
+
   it('.kindFilter() filters by exact kind', () => {
     const rows = new NodeQuery().kindFilter('class').all(db);
     expect(rows.length).toBe(1);