diff --git a/src/resources/extensions/gsd/commands-codebase.ts b/src/resources/extensions/gsd/commands-codebase.ts
index 305f09256..0072d806a 100644
--- a/src/resources/extensions/gsd/commands-codebase.ts
+++ b/src/resources/extensions/gsd/commands-codebase.ts
@@ -14,14 +14,21 @@ import {
   getCodebaseMapStats,
   readCodebaseMap,
 } from "./codebase-generator.js";
+import { loadEffectiveGSDPreferences } from "./preferences.js";
+import type { CodebaseMapOptions } from "./codebase-generator.js";
 
 const USAGE =
   "Usage: /gsd codebase [generate|update|stats]\n\n" +
-  "  generate [--max-files N]  — Generate or regenerate CODEBASE.md\n" +
-  "  update                    — Incremental update (preserves descriptions)\n" +
-  "  stats                     — Show file count, coverage, and generation time\n" +
-  "  help                      — Show this help\n\n" +
-  "With no subcommand, shows stats if a map exists or help if not.";
+  "  generate [--max-files N] [--collapse-threshold N]  — Generate or regenerate CODEBASE.md\n" +
+  "  update [--max-files N] [--collapse-threshold N]    — Incremental update (preserves descriptions)\n" +
+  "  stats                                              — Show file count, coverage, and generation time\n" +
+  "  help                                               — Show this help\n\n" +
+  "With no subcommand, shows stats if a map exists or help if not.\n\n" +
+  "Configure defaults via preferences.md:\n" +
+  "  codebase:\n" +
+  "    exclude_patterns: [\"docs/\", \"fixtures/\"]\n" +
+  "    max_files: 1000\n" +
+  "    collapse_threshold: 15";
 
 export async function handleCodebase(
   args: string,
@@ -34,15 +41,15 @@ export async function handleCodebase(
 
   switch (sub) {
     case "generate": {
-      const maxFiles = parseMaxFiles(args, ctx);
-      if (maxFiles === false) return; // validation failed, message already shown
+      const options = resolveCodebaseOptions(args, ctx);
+      if (options === false) return; // validation failed, message already shown
 
       const existing = readCodebaseMap(basePath);
       const existingDescriptions = existing
         ? (await import("./codebase-generator.js")).parseCodebaseMap(existing)
         : undefined;
 
-      const result = generateCodebaseMap(basePath, { maxFiles: maxFiles ?? undefined }, existingDescriptions);
+      const result = generateCodebaseMap(basePath, options, existingDescriptions);
 
       if (result.fileCount === 0) {
         ctx.ui.notify(
@@ -73,10 +80,10 @@ export async function handleCodebase(
         return;
       }
 
-      const maxFiles = parseMaxFiles(args, ctx);
-      if (maxFiles === false) return;
+      const options = resolveCodebaseOptions(args, ctx);
+      if (options === false) return;
 
-      const result = updateCodebaseMap(basePath, { maxFiles: maxFiles ?? undefined });
+      const result = updateCodebaseMap(basePath, options);
       writeCodebaseMap(basePath, result.content);
 
       ctx.ui.notify(
@@ -141,19 +148,44 @@ function showStats(basePath: string, ctx: ExtensionCommandContext): void {
 }
 
 /**
- * Parse and validate --max-files flag.
- * Returns the parsed number, undefined if flag not present, or false if invalid.
+ * Resolve codebase map options by merging preferences with CLI flags.
+ * CLI flags override preferences; preferences override built-in defaults.
+ * Returns false if validation failed (error already shown to user).
  */
-function parseMaxFiles(args: string, ctx: ExtensionCommandContext): number | undefined | false {
-  const maxFilesStr = extractFlag(args, "--max-files");
-  if (!maxFilesStr) return undefined;
+function resolveCodebaseOptions(args: string, ctx: ExtensionCommandContext): CodebaseMapOptions | false {
+  // Load preferences defaults
+  const prefs = loadEffectiveGSDPreferences()?.preferences?.codebase;
 
-  const maxFiles = parseInt(maxFilesStr, 10);
-  if (isNaN(maxFiles) || maxFiles < 1) {
-    ctx.ui.notify("--max-files must be a positive integer (e.g. --max-files 200).", "warning");
-    return false;
+  // Parse CLI flags
+  const maxFilesStr = extractFlag(args, "--max-files");
+  const collapseStr = extractFlag(args, "--collapse-threshold");
+
+  // Validate --max-files
+  let maxFiles: number | undefined;
+  if (maxFilesStr) {
+    maxFiles = parseInt(maxFilesStr, 10);
+    if (isNaN(maxFiles) || maxFiles < 1) {
+      ctx.ui.notify("--max-files must be a positive integer (e.g. --max-files 200).", "warning");
+      return false;
+    }
   }
-  return maxFiles;
+
+  // Validate --collapse-threshold
+  let collapseThreshold: number | undefined;
+  if (collapseStr) {
+    collapseThreshold = parseInt(collapseStr, 10);
+    if (isNaN(collapseThreshold) || collapseThreshold < 1) {
+      ctx.ui.notify("--collapse-threshold must be a positive integer (e.g. --collapse-threshold 15).", "warning");
+      return false;
+    }
+  }
+
+  return {
+    // CLI flags override preferences
+    maxFiles: maxFiles ?? prefs?.max_files,
+    collapseThreshold: collapseThreshold ?? prefs?.collapse_threshold,
+    excludePatterns: prefs?.exclude_patterns,
+  };
 }
 
 function extractFlag(args: string, flag: string): string | undefined {
diff --git a/src/resources/extensions/gsd/commands/catalog.ts b/src/resources/extensions/gsd/commands/catalog.ts
index 02882a07c..06b614173 100644
--- a/src/resources/extensions/gsd/commands/catalog.ts
+++ b/src/resources/extensions/gsd/commands/catalog.ts
@@ -229,8 +229,10 @@ const NESTED_COMPLETIONS: CompletionMap = {
   codebase: [
     { cmd: "generate", desc: "Generate or regenerate CODEBASE.md" },
     { cmd: "generate --max-files", desc: "Generate with custom file limit (default: 500)" },
+    { cmd: "generate --collapse-threshold", desc: "Generate with custom collapse threshold (default: 20)" },
     { cmd: "update", desc: "Incremental update (preserves descriptions)" },
     { cmd: "update --max-files", desc: "Update with custom file limit" },
+    { cmd: "update --collapse-threshold", desc: "Update with custom collapse threshold" },
     { cmd: "stats", desc: "Show file count, description coverage, and generation time" },
     { cmd: "help", desc: "Show usage and available subcommands" },
   ],
diff --git a/src/resources/extensions/gsd/init-wizard.ts b/src/resources/extensions/gsd/init-wizard.ts
index f1a077dd8..d5f490459 100644
--- a/src/resources/extensions/gsd/init-wizard.ts
+++ b/src/resources/extensions/gsd/init-wizard.ts
@@ -16,6 +16,7 @@ import { gsdRoot } from "./paths.js";
 import { assertSafeDirectory } from "./validate-directory.js";
 import type { ProjectDetection, ProjectSignals } from "./detection.js";
 import { runSkillInstallStep } from "./skill-catalog.js";
+import { generateCodebaseMap, writeCodebaseMap } from "./codebase-generator.js";
 
 // ─── Types ──────────────────────────────────────────────────────────────────────
 
@@ -238,6 +239,17 @@ export async function showProjectInit(
   ensureGitignore(basePath);
   untrackRuntimeFiles(basePath);
 
+  // Auto-generate codebase map for instant agent orientation
+  try {
+    const result = generateCodebaseMap(basePath);
+    if (result.fileCount > 0) {
+      writeCodebaseMap(basePath, result.content);
+      ctx.ui.notify(`Codebase map generated: ${result.fileCount} files`, "info");
+    }
+  } catch {
+    // Non-fatal — codebase map generation failure should never block project init
+  }
+
   ctx.ui.notify("GSD initialized. Starting your first milestone...", "info");
 
   return { completed: true, bootstrapped: true };
diff --git a/src/resources/extensions/gsd/preferences-types.ts b/src/resources/extensions/gsd/preferences-types.ts
index 4356badca..dd87949d4 100644
--- a/src/resources/extensions/gsd/preferences-types.ts
+++ b/src/resources/extensions/gsd/preferences-types.ts
@@ -103,6 +103,7 @@ export const KNOWN_PREFERENCE_KEYS = new Set<string>([
   "stale_commit_threshold_minutes",
   "context_management",
   "experimental",
+  "codebase",
 ]);
 
 /** Canonical list of all dispatch unit types. */
@@ -211,6 +212,16 @@ export interface ExperimentalPreferences {
   rtk?: boolean;
 }
 
+/** Configuration for the codebase map generator (/gsd codebase). */
+export interface CodebaseMapPreferences {
+  /** Additional directory/file patterns to exclude (e.g. ["docs/", "fixtures/"]). Merged with built-in defaults. */
+  exclude_patterns?: string[];
+  /** Max files to include in the map. Default: 500. */
+  max_files?: number;
+  /** Files-per-directory threshold before collapsing to a summary line. Default: 20. */
+  collapse_threshold?: number;
+}
+
 export interface GSDPreferences {
   version?: number;
   mode?: WorkflowMode;
@@ -275,6 +286,8 @@ export interface GSDPreferences {
    * See the preferences reference for details on each feature.
    */
   experimental?: ExperimentalPreferences;
+  /** Configuration for the codebase map generator (/gsd codebase). */
+  codebase?: CodebaseMapPreferences;
 }
 
 export interface LoadedGSDPreferences {
diff --git a/src/resources/extensions/gsd/preferences.ts b/src/resources/extensions/gsd/preferences.ts
index 50a08a937..93ac6f1f0 100644
--- a/src/resources/extensions/gsd/preferences.ts
+++ b/src/resources/extensions/gsd/preferences.ts
@@ -49,6 +49,7 @@ export type {
   AutoSupervisorConfig,
   RemoteQuestionsConfig,
   CmuxPreferences,
+  CodebaseMapPreferences,
   GSDPreferences,
   LoadedGSDPreferences,
   SkillResolution,
@@ -372,6 +373,17 @@ function mergePreferences(base: GSDPreferences, override: GSDPreferences): GSDPr
     service_tier: override.service_tier ?? base.service_tier,
     forensics_dedup: override.forensics_dedup ?? base.forensics_dedup,
     show_token_cost: override.show_token_cost ?? base.show_token_cost,
+    codebase: (base.codebase || override.codebase)
+      ? {
+          ...(base.codebase ?? {}),
+          ...(override.codebase ?? {}),
+          // Merge exclude_patterns arrays rather than overriding
+          exclude_patterns: [
+            ...((base.codebase?.exclude_patterns) ?? []),
+            ...((override.codebase?.exclude_patterns) ?? []),
+          ].filter(Boolean),
+        }
+      : undefined,
   };
 }
 
diff --git a/src/resources/extensions/gsd/tests/codebase-generator.test.ts b/src/resources/extensions/gsd/tests/codebase-generator.test.ts
index c698fc65f..91ef3314a 100644
--- a/src/resources/extensions/gsd/tests/codebase-generator.test.ts
+++ b/src/resources/extensions/gsd/tests/codebase-generator.test.ts
@@ -486,3 +486,66 @@ test("getCodebaseMapStats: reads total file count from header for accuracy with
     cleanup(base);
   }
 });
+
+// ─── excludePatterns from options ────────────────────────────────────────
+
+test("generateCodebaseMap: custom excludePatterns filters additional directories", () => {
+  const base = makeTmpRepo();
+  try {
+    addFile(base, "src/main.ts");
+    addFile(base, "src/utils.ts");
+    addFile(base, ".cache-data/data/index.lance");
+    addFile(base, "docs/guide.md");
+
+    const result = generateCodebaseMap(base, {
+      excludePatterns: [".cache-data/", "docs/"],
+    });
+    assert.ok(result.content.includes("`src/main.ts`"));
+    assert.ok(result.content.includes("`src/utils.ts`"));
+    assert.ok(!result.content.includes(".cache-data"));
+    assert.ok(!result.content.includes("guide.md"));
+    assert.equal(result.fileCount, 2);
+  } finally {
+    cleanup(base);
+  }
+});
+
+test("generateCodebaseMap: collapseThreshold option overrides default", () => {
+  const base = makeTmpRepo();
+  try {
+    // Create 10 files in one directory — below default threshold (20)
+    // but above a custom threshold of 5
+    for (let i = 0; i < 10; i++) {
+      addFile(base, `src/comp${i}.ts`);
+    }
+
+    // With default threshold (20), files should NOT collapse
+    const expanded = generateCodebaseMap(base);
+    assert.ok(expanded.content.includes("`src/comp0.ts`"));
+
+    // With custom threshold (5), files SHOULD collapse
+    const collapsed = generateCodebaseMap(base, { collapseThreshold: 5 });
+    assert.ok(collapsed.content.includes("10 files"));
+    assert.ok(!collapsed.content.includes("`src/comp0.ts`\n"));
+  } finally {
+    cleanup(base);
+  }
+});
+
+test("updateCodebaseMap: respects excludePatterns option", () => {
+  const base = makeTmpRepo();
+  try {
+    addFile(base, "src/main.ts");
+    addFile(base, "vendor-extra/lib.js");
+
+    const initial = generateCodebaseMap(base);
+    writeCodebaseMap(base, initial.content);
+
+    // Update with exclusion should remove vendor-extra files
+    const result = updateCodebaseMap(base, { excludePatterns: ["vendor-extra/"] });
+    assert.ok(result.content.includes("`src/main.ts`"));
+    assert.ok(!result.content.includes("vendor-extra"));
+  } finally {
+    cleanup(base);
+  }
+});