diff --git a/skillhub-cli/src/commands/archive.ts b/skillhub-cli/src/commands/archive.ts
index 46052e72..6741a78d 100644
--- a/skillhub-cli/src/commands/archive.ts
+++ b/skillhub-cli/src/commands/archive.ts
@@ -1,7 +1,7 @@
 import { Command } from "commander";
 import { ApiClient } from "../core/api-client.js";
 import { requireToken } from "../core/auth-token.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 import { success, error } from "../utils/logger.js";
 import { parseSkillName } from "../core/skill-name.js";
 
@@ -27,7 +27,7 @@ export function registerArchive(program: Command) {
 
       try {
         const token = await requireToken();
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const client = new ApiClient({ baseUrl: config.registry, token });
         await client.post(`/api/v1/skills/${namespace}/${skillSlug}/archive`);
         success(`Archived ${skillSlug}`);
diff --git a/skillhub-cli/src/commands/delete.ts b/skillhub-cli/src/commands/delete.ts
index dd338c6b..a535ec29 100644
--- a/skillhub-cli/src/commands/delete.ts
+++ b/skillhub-cli/src/commands/delete.ts
@@ -1,7 +1,7 @@
 import { Command } from "commander";
 import { ApiClient } from "../core/api-client.js";
 import { requireToken } from "../core/auth-token.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 import { success, error } from "../utils/logger.js";
 import { parseSkillName } from "../core/skill-name.js";
 
@@ -28,7 +28,7 @@ export function registerDelete(program: Command) {
 
       try {
         const token = await requireToken();
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const client = new ApiClient({ baseUrl: config.registry, token });
         await client.delete(`/api/v1/skills/${namespace}/${skillSlug}`);
         success(`Deleted ${skillSlug} from ${namespace}`);
diff --git a/skillhub-cli/src/commands/download.ts b/skillhub-cli/src/commands/download.ts
index 8b6e27d7..54db14a6 100644
--- a/skillhub-cli/src/commands/download.ts
+++ b/skillhub-cli/src/commands/download.ts
@@ -4,7 +4,7 @@ import { resolve } from "node:path";
 import { finished } from "node:stream/promises";
 import { ApiClient } from "../core/api-client.js";
 import { ApiRoutes } from "../schema/routes.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 import { readToken } from "../core/auth-token.js";
 import { success, error } from "../utils/logger.js";
 import { parseSkillName } from "../core/skill-name.js";
@@ -19,7 +19,7 @@ export function registerDownload(program: Command) {
     .option("--output <dir>", "Output directory")
     .action(async (slug: string, opts: Record<string, string>) => {
       const { namespace, slug: skillSlug } = parseSkillName(slug);
-      const config = loadConfig();
+      const config = loadConfigFromProgram(program);
       const token = await readToken();
       const client = new ApiClient({ baseUrl: config.registry, token: token || undefined });
 
diff --git a/skillhub-cli/src/commands/explore.ts b/skillhub-cli/src/commands/explore.ts
index dba7576c..cd60d57f 100644
--- a/skillhub-cli/src/commands/explore.ts
+++ b/skillhub-cli/src/commands/explore.ts
@@ -1,6 +1,6 @@
 import { Command } from "commander";
 import { ApiClient } from "../core/api-client.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 import { readToken } from "../core/auth-token.js";
 import { ApiRoutes } from "../schema/routes.js";
 import { info, dim } from "../utils/logger.js";
@@ -222,7 +222,7 @@ export function registerExplore(program: Command) {
     .option("-n, --limit <n>", "Max results", "20")
     .option("-s, --sort <sort>", "Sort by: hot, newest, downloads (default: interactive mode)")
     .action(async (query: string | undefined, opts: { limit: string; sort?: string }) => {
-      const config = loadConfig();
+      const config = loadConfigFromProgram(program);
       const token = await readToken();
       const client = new ApiClient({ baseUrl: config.registry, token: token || undefined });
       const sortMap: Record<string, string> = { hot: "rating", newest: "newest", downloads: "downloads" };
diff --git a/skillhub-cli/src/commands/hide.ts b/skillhub-cli/src/commands/hide.ts
index 7863c43c..d647e3f2 100644
--- a/skillhub-cli/src/commands/hide.ts
+++ b/skillhub-cli/src/commands/hide.ts
@@ -1,7 +1,7 @@
 import { Command } from "commander";
 import { ApiClient } from "../core/api-client.js";
 import { requireToken } from "../core/auth-token.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 import { success, error } from "../utils/logger.js";
 import { parseSkillName } from "../core/skill-name.js";
 
@@ -27,7 +27,7 @@ export function registerHide(program: Command) {
 
       try {
         const token = await requireToken();
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const client = new ApiClient({ baseUrl: config.registry, token });
 
         const detail = await client.get<{ id: number }>(
@@ -67,7 +67,7 @@ export function registerHide(program: Command) {
 
       try {
         const token = await requireToken();
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const client = new ApiClient({ baseUrl: config.registry, token });
 
         const detail = await client.get<{ id: number }>(
diff --git a/skillhub-cli/src/commands/inspect.ts b/skillhub-cli/src/commands/inspect.ts
index 8acbea8e..f68ca0ee 100644
--- a/skillhub-cli/src/commands/inspect.ts
+++ b/skillhub-cli/src/commands/inspect.ts
@@ -1,7 +1,7 @@
 import { Command } from "commander";
 import { ApiClient } from "../core/api-client.js";
 import { ApiRoutes } from "../schema/routes.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 import { readToken } from "../core/auth-token.js";
 import { parseSkillName } from "../core/skill-name.js";
 import { info, dim, error } from "../utils/logger.js";
@@ -70,7 +70,7 @@ export function registerInspect(program: Command) {
     .description("View skill metadata without installing")
     .option("--namespace <ns>", "Search in specific namespace (searches all if not specified)")
     .action(async (slug: string, opts: { namespace?: string }) => {
-      const config = loadConfig();
+      const config = loadConfigFromProgram(program);
       const token = await readToken();
       const client = new ApiClient({ baseUrl: config.registry, token: token || undefined });
 
diff --git a/skillhub-cli/src/commands/install.ts b/skillhub-cli/src/commands/install.ts
index 4a272a4f..7062e52b 100644
--- a/skillhub-cli/src/commands/install.ts
+++ b/skillhub-cli/src/commands/install.ts
@@ -4,7 +4,7 @@ import { tmpdir } from "node:os";
 import { join } from "node:path";
 import { createWriteStream, createReadStream, existsSync, mkdirSync } from "node:fs";
 import { ApiClient } from "../core/api-client.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfigFromProgram } from "../core/config.js";
 import { readToken } from "../core/auth-token.js";
 import { discoverSkills } from "../core/skill-discovery.js";
 import { installSkill } from "../core/installer.js";
@@ -227,9 +227,9 @@ export function registerInstall(program: Command) {
 
       try {
         if (effectiveSource === "registry") {
-          await installFromRegistry(source, opts, spinner);
+          await installFromRegistry(source, opts, spinner, program);
         } else {
-          await installFromGit(source, installSource, effectiveSource, opts, spinner);
+          await installFromGit(source, installSource, effectiveSource, opts, spinner, program);
         }
       } catch (e: any) {
         spinner.fail(e.message);
@@ -238,7 +238,12 @@ export function registerInstall(program: Command) {
     });
 }
 
-async function installFromRegistry(slug: string, opts: Record<string, string | string[] | boolean>, spinner: any) {
+async function installFromRegistry(
+  slug: string,
+  opts: Record<string, string | string[] | boolean>,
+  spinner: any,
+  program: Command
+) {
   let ns = "global";
   let actualSlug = slug;
   let userSpecifiedNamespace = false;
@@ -252,7 +257,7 @@ async function installFromRegistry(slug: string, opts: Record<string, string | s
     }
   }
 
-  const config = loadConfig();
+  const config = loadConfigFromProgram(program);
   const token = await readToken();
   const client = new ApiClient({ baseUrl: config.registry, token: token || undefined });
 
@@ -581,7 +586,14 @@ async function installFromRegistry(slug: string, opts: Record<string, string | s
   await rm(tmpDir, { recursive: true, force: true });
 }
 
-async function installFromGit(skillName: string, source: string, sourceType: SourceType, opts: Record<string, string | string[] | boolean>, spinner: any) {
+async function installFromGit(
+  skillName: string,
+  source: string,
+  sourceType: SourceType,
+  opts: Record<string, string | string[] | boolean>,
+  spinner: any,
+  program: Command
+) {
   let skillsDir: string;
 
   const parsed = parseSource(source);
diff --git a/skillhub-cli/src/commands/me.ts b/skillhub-cli/src/commands/me.ts
index 9fb52ba1..015e5ed3 100644
--- a/skillhub-cli/src/commands/me.ts
+++ b/skillhub-cli/src/commands/me.ts
@@ -1,6 +1,6 @@
 import { Command } from "commander";
 import { ApiClient } from "../core/api-client.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 import { requireToken } from "../core/auth-token.js";
 import { error, info, dim } from "../utils/logger.js";
 
@@ -33,7 +33,7 @@ export function registerMe(program: Command) {
     .action(async () => {
       try {
         const token = await requireToken();
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const client = new ApiClient({ baseUrl: config.registry, token });
         const resp = await client.get<MeSkillsResponse>("/api/v1/me/skills");
         const skills = resp.items || [];
@@ -63,7 +63,7 @@ export function registerMe(program: Command) {
     .action(async () => {
       try {
         const token = await requireToken();
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const client = new ApiClient({ baseUrl: config.registry, token });
         const resp = await client.get<MeSkillsResponse>("/api/v1/me/stars");
         const skills = resp.items || [];
diff --git a/skillhub-cli/src/commands/namespaces.ts b/skillhub-cli/src/commands/namespaces.ts
index 8359c5ee..942bdb10 100644
--- a/skillhub-cli/src/commands/namespaces.ts
+++ b/skillhub-cli/src/commands/namespaces.ts
@@ -2,7 +2,7 @@ import { Command } from "commander";
 import { ApiClient } from "../core/api-client.js";
 import { ApiRoutes, NamespaceResponse } from "../schema/routes.js";
 import { requireToken } from "../core/auth-token.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 import { error } from "../utils/logger.js";
 
 export function registerNamespaces(program: Command) {
@@ -12,7 +12,7 @@ export function registerNamespaces(program: Command) {
     .action(async () => {
       try {
         const token = await requireToken();
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const client = new ApiClient({ baseUrl: config.registry, token });
         const namespaces = await client.get<NamespaceResponse[]>(ApiRoutes.meNamespaces);
         const isJson = program.opts().json;
diff --git a/skillhub-cli/src/commands/notifications.ts b/skillhub-cli/src/commands/notifications.ts
index 2fd73ec8..fe341ee6 100644
--- a/skillhub-cli/src/commands/notifications.ts
+++ b/skillhub-cli/src/commands/notifications.ts
@@ -1,6 +1,6 @@
 import { Command } from "commander";
 import { ApiClient } from "../core/api-client.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 import { requireToken } from "../core/auth-token.js";
 import { success, error, info, dim } from "../utils/logger.js";
 
@@ -26,7 +26,7 @@ export function registerNotifications(program: Command) {
     .action(async (opts: { unread?: boolean }) => {
       try {
         const token = await requireToken();
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const client = new ApiClient({ baseUrl: config.registry, token });
         const notifs = await client.get<Notification[]>("/api/v1/notifications");
         const filtered = opts.unread ? notifs.filter((n) => !n.read) : notifs;
@@ -50,7 +50,7 @@ export function registerNotifications(program: Command) {
     .action(async (id: string) => {
       try {
         const token = await requireToken();
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const client = new ApiClient({ baseUrl: config.registry, token });
         await client.put(`/api/v1/notifications/${id}/read`);
         success(`Marked notification ${id} as read`);
@@ -66,7 +66,7 @@ export function registerNotifications(program: Command) {
     .action(async () => {
       try {
         const token = await requireToken();
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const client = new ApiClient({ baseUrl: config.registry, token });
         await client.put("/api/v1/notifications/read-all");
         success("All notifications marked as read");
diff --git a/skillhub-cli/src/commands/publish.ts b/skillhub-cli/src/commands/publish.ts
index 8f62822b..0ccd41f7 100644
--- a/skillhub-cli/src/commands/publish.ts
+++ b/skillhub-cli/src/commands/publish.ts
@@ -5,7 +5,7 @@ import { FormData } from "undici";
 import { ApiClient } from "../core/api-client.js";
 import { ApiRoutes, PublishResponse } from "../schema/routes.js";
 import { requireToken } from "../core/auth-token.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 import { success, error, info } from "../utils/logger.js";
 import ora from "ora";
 import semver from "semver";
@@ -49,7 +49,7 @@ export function registerPublish(program: Command) {
 
       try {
         const token = await requireToken();
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const client = new ApiClient({ baseUrl: config.registry, token });
 
         const spinner = ora(`Publishing ${slug}@${version} to ${namespace}`).start();
diff --git a/skillhub-cli/src/commands/rating.ts b/skillhub-cli/src/commands/rating.ts
index 583d4f6a..92fcd173 100644
--- a/skillhub-cli/src/commands/rating.ts
+++ b/skillhub-cli/src/commands/rating.ts
@@ -1,6 +1,6 @@
 import { Command } from "commander";
 import { ApiClient } from "../core/api-client.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 import { requireToken } from "../core/auth-token.js";
 import { success, error, info, dim } from "../utils/logger.js";
 import { parseSkillName } from "../core/skill-name.js";
@@ -13,7 +13,7 @@ export function registerRating(program: Command) {
       try {
         const { namespace, slug: skillSlug } = parseSkillName(slug);
         const token = await requireToken();
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const client = new ApiClient({ baseUrl: config.registry, token });
 
         const detail = await client.get<{ id: number }>(
@@ -51,7 +51,7 @@ export function registerRate(program: Command) {
       try {
         const { namespace, slug: skillSlug } = parseSkillName(slug);
         const token = await requireToken();
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const client = new ApiClient({ baseUrl: config.registry, token });
 
         const detail = await client.get<{ id: number }>(
diff --git a/skillhub-cli/src/commands/report.ts b/skillhub-cli/src/commands/report.ts
index 91c3e14c..f20c6d87 100644
--- a/skillhub-cli/src/commands/report.ts
+++ b/skillhub-cli/src/commands/report.ts
@@ -2,7 +2,7 @@ import { Command } from "commander";
 import { createInterface } from "node:readline";
 import { ApiClient } from "../core/api-client.js";
 import { requireToken } from "../core/auth-token.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 import { success, error } from "../utils/logger.js";
 import { parseSkillName } from "../core/skill-name.js";
 
@@ -15,7 +15,7 @@ export function registerReport(program: Command) {
       try {
         const { namespace, slug: skillSlug } = parseSkillName(slug);
         const token = await requireToken();
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const client = new ApiClient({ baseUrl: config.registry, token });
 
         let reason = opts.reason;
diff --git a/skillhub-cli/src/commands/resolve.ts b/skillhub-cli/src/commands/resolve.ts
index 348f564b..6d83ce2a 100644
--- a/skillhub-cli/src/commands/resolve.ts
+++ b/skillhub-cli/src/commands/resolve.ts
@@ -1,6 +1,6 @@
 import { Command } from "commander";
 import { ApiClient } from "../core/api-client.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 import { readToken } from "../core/auth-token.js";
 import { success, error, info, dim } from "../utils/logger.js";
 import { parseSkillName } from "../core/skill-name.js";
@@ -51,7 +51,7 @@ export function registerResolve(program: Command) {
     .action(async (slug: string, opts: Record<string, string>) => {
       try {
         const { namespace, slug: skillSlug } = parseSkillName(slug);
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const token = await readToken();
         const client = new ApiClient({ baseUrl: config.registry, token: token || undefined });
 
diff --git a/skillhub-cli/src/commands/reviews.ts b/skillhub-cli/src/commands/reviews.ts
index ba38ca14..911777e0 100644
--- a/skillhub-cli/src/commands/reviews.ts
+++ b/skillhub-cli/src/commands/reviews.ts
@@ -1,7 +1,7 @@
 import { Command } from "commander";
 import { ApiClient } from "../core/api-client.js";
 import { requireToken } from "../core/auth-token.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 import { success, error, info, dim } from "../utils/logger.js";
 
 export interface ReviewSubmission {
@@ -24,7 +24,7 @@ export function registerReviews(program: Command) {
     .action(async () => {
       try {
         const token = await requireToken();
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const client = new ApiClient({ baseUrl: config.registry, token });
         const submissions = await client.get<ReviewSubmission[]>("/api/v1/reviews/my-submissions");
         if (!submissions || submissions.length === 0) {
diff --git a/skillhub-cli/src/commands/search.ts b/skillhub-cli/src/commands/search.ts
index 47e4b482..70c96ddd 100644
--- a/skillhub-cli/src/commands/search.ts
+++ b/skillhub-cli/src/commands/search.ts
@@ -1,7 +1,7 @@
 import { Command } from "commander";
 import { ApiClient } from "../core/api-client.js";
 import { ApiRoutes, SearchResponse } from "../schema/routes.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 import { readToken } from "../core/auth-token.js";
 import { error, dim } from "../utils/logger.js";
 
@@ -12,7 +12,7 @@ export function registerSearch(program: Command) {
     .option("-n, --limit <n>", "Max results", "20")
     .option("--namespace <ns>", "Filter by namespace")
     .action(async (query: string[], opts: { limit: string; namespace?: string }) => {
-      const config = loadConfig();
+      const config = loadConfigFromProgram(program);
       const token = await readToken();
       const client = new ApiClient({ baseUrl: config.registry, token: token || undefined });
 
diff --git a/skillhub-cli/src/commands/star.ts b/skillhub-cli/src/commands/star.ts
index 067e2c1a..26651965 100644
--- a/skillhub-cli/src/commands/star.ts
+++ b/skillhub-cli/src/commands/star.ts
@@ -2,7 +2,7 @@ import { Command } from "commander";
 import { ApiClient } from "../core/api-client.js";
 import { ApiRoutes } from "../schema/routes.js";
 import { requireToken } from "../core/auth-token.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 import { success, error } from "../utils/logger.js";
 import { parseSkillName } from "../core/skill-name.js";
 
@@ -15,7 +15,7 @@ export function registerStar(program: Command) {
       try {
         const { namespace, slug: skillSlug } = parseSkillName(slug);
         const token = await requireToken();
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const client = new ApiClient({ baseUrl: config.registry, token });
 
         const detailPath = ApiRoutes.skillDetail.replace("{namespace}", namespace).replace("{slug}", skillSlug);
diff --git a/skillhub-cli/src/commands/sync.ts b/skillhub-cli/src/commands/sync.ts
index 9ded9ae6..7f87bbb8 100644
--- a/skillhub-cli/src/commands/sync.ts
+++ b/skillhub-cli/src/commands/sync.ts
@@ -5,7 +5,7 @@ import { FormData } from "undici";
 import { existsSync } from "node:fs";
 import { discoverSkills } from "../core/skill-discovery.js";
 import { requireToken } from "../core/auth-token.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 import { ApiClient } from "../core/api-client.js";
 import { ApiRoutes } from "../schema/routes.js";
 import { info, dim, success, error } from "../utils/logger.js";
@@ -36,7 +36,7 @@ export function registerSync(program: Command) {
 
       try {
         const token = await requireToken();
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const client = new ApiClient({ baseUrl: config.registry, token });
 
         info(`Scanning ${scanPath} for skills...`);
diff --git a/skillhub-cli/src/commands/transfer.ts b/skillhub-cli/src/commands/transfer.ts
index b54684e1..92c983a9 100644
--- a/skillhub-cli/src/commands/transfer.ts
+++ b/skillhub-cli/src/commands/transfer.ts
@@ -2,7 +2,7 @@ import { Command } from "commander";
 import { ApiClient } from "../core/api-client.js";
 import { ApiRoutes } from "../schema/routes.js";
 import { requireToken } from "../core/auth-token.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 import { success, error } from "../utils/logger.js";
 
 export function registerTransfer(program: Command) {
@@ -26,7 +26,7 @@ export function registerTransfer(program: Command) {
 
       try {
         const token = await requireToken();
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const client = new ApiClient({ baseUrl: config.registry, token });
         await client.post(ApiRoutes.namespaceTransferOwnership.replace("{namespace}", namespace), { body: JSON.stringify({ newOwnerId }) });
         success(`Ownership of ${namespace} transferred to ${newOwnerId}`);
diff --git a/skillhub-cli/src/commands/versions.ts b/skillhub-cli/src/commands/versions.ts
index bc0e9de5..4177e2be 100644
--- a/skillhub-cli/src/commands/versions.ts
+++ b/skillhub-cli/src/commands/versions.ts
@@ -1,7 +1,7 @@
 import { Command } from "commander";
 import { ApiClient } from "../core/api-client.js";
 import { readToken } from "../core/auth-token.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 import { error, info, dim, success } from "../utils/logger.js";
 import { parseSkillName } from "../core/skill-name.js";
 import { searchSkills, runInteractiveSearch } from "../core/interactive-search.js";
@@ -37,7 +37,7 @@ export function registerVersions(program: Command) {
     .action(async (slug: string) => {
       try {
         const { namespace, slug: skillSlug } = parseSkillName(slug);
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const token = await readToken();
         const client = new ApiClient({ baseUrl: config.registry, token: token || undefined });
 
diff --git a/skillhub-cli/src/commands/whoami.ts b/skillhub-cli/src/commands/whoami.ts
index 3aa2954a..dbb77ad2 100644
--- a/skillhub-cli/src/commands/whoami.ts
+++ b/skillhub-cli/src/commands/whoami.ts
@@ -3,7 +3,7 @@ import { ApiClient } from "../core/api-client.js";
 import { ApiRoutes, WhoamiResponse } from "../schema/routes.js";
 import { requireToken } from "../core/auth-token.js";
 import { success, error } from "../utils/logger.js";
-import { loadConfig } from "../core/config.js";
+import { loadConfig, loadConfigFromProgram } from "../core/config.js";
 
 export function registerWhoami(program: Command) {
   program
@@ -12,7 +12,7 @@ export function registerWhoami(program: Command) {
     .action(async () => {
       try {
         const token = await requireToken();
-        const config = loadConfig();
+        const config = loadConfigFromProgram(program);
         const client = new ApiClient({ baseUrl: config.registry, token });
         const resp = await client.get<WhoamiResponse>(ApiRoutes.whoami);
         const isJson = program.opts().json;
diff --git a/skillhub-cli/src/core/config.ts b/skillhub-cli/src/core/config.ts
index bbfd3009..fd42523d 100644
--- a/skillhub-cli/src/core/config.ts
+++ b/skillhub-cli/src/core/config.ts
@@ -1,6 +1,7 @@
 import { existsSync, readFileSync, writeFileSync, mkdirSync } from "node:fs";
 import { homedir } from "node:os";
 import { join } from "node:path";
+import type { Command } from "commander";
 
 const CONFIG_DIR = join(homedir(), ".skillhub");
 const CONFIG_FILE = join(CONFIG_DIR, "config.json");
@@ -14,24 +15,43 @@ const DEFAULT_CONFIG: CliConfig = {
   registry: "http://localhost:8080",
 };
 
-export function loadConfig(): CliConfig {
+export function loadConfig(overrides?: Partial<CliConfig>): CliConfig {
+  // Priority: overrides > env > config file > defaults
   const envRegistry = process.env.SKILLHUB_REGISTRY;
-  if (envRegistry) {
-    if (!existsSync(CONFIG_FILE)) return { registry: envRegistry };
+  const baseConfig: CliConfig = envRegistry
+    ? { registry: envRegistry }
+    : { ...DEFAULT_CONFIG };
+
+  if (existsSync(CONFIG_FILE)) {
     try {
       const raw = readFileSync(CONFIG_FILE, "utf-8");
-      return { registry: envRegistry, ...JSON.parse(raw) };
+      Object.assign(baseConfig, JSON.parse(raw));
     } catch {
-      return { registry: envRegistry };
+      // Use base config if file is invalid
     }
   }
-  if (!existsSync(CONFIG_FILE)) return { ...DEFAULT_CONFIG };
-  try {
-    const raw = readFileSync(CONFIG_FILE, "utf-8");
-    return { ...DEFAULT_CONFIG, ...JSON.parse(raw) };
-  } catch {
-    return { ...DEFAULT_CONFIG };
+
+  // Apply overrides (e.g., from command-line options)
+  if (overrides) {
+    Object.assign(baseConfig, overrides);
   }
+
+  return baseConfig;
+}
+
+/**
+ * Helper function to load config with command-line options from Commander.js program
+ * Use this in command actions to get config that respects --registry flag
+ */
+export function loadConfigFromProgram(program: Command): CliConfig {
+  const opts = program.opts();
+  const overrides: Partial<CliConfig> = {};
+
+  if (opts.registry) {
+    overrides.registry = opts.registry as string;
+  }
+
+  return loadConfig(overrides);
 }
 
 export function saveConfig(config: Partial<CliConfig>): void {