diff --git a/.changeset/fluffy-lines-visit.md b/.changeset/fluffy-lines-visit.md
new file mode 100644
index 0000000..1662747
--- /dev/null
+++ b/.changeset/fluffy-lines-visit.md
@@ -0,0 +1,14 @@
+---
+"@mixedbread/cli": patch
+---
+
+Improved CLI I/O, concurrency, and code deduplication
+
+- Routed log and spinner output to stderr to keep stdout clean for piped data
+- Replaced internal `mergeCommandOptions` with Commander's built-in `optsWithGlobals()`
+- Switched to sliding-window concurrency (`p-limit`) for file uploads
+- Used async file I/O in upload and sync hot paths
+- Extracted shared `checkExistingFiles` utility
+- Fixed missing `process.exit(1)` in completion command error handlers
+- Fixed spinners not being stopped in catch blocks for sync and upload commands
+- Changed `formatBytes` to return `"-"` instead of `"0 B"` for undefined/NaN values
diff --git a/packages/cli/package.json b/packages/cli/package.json
index 1888137..1b63e49 100644
--- a/packages/cli/package.json
+++ b/packages/cli/package.json
@@ -55,7 +55,6 @@
     "chalk": "^5.6.2",
     "cli-table3": "^0.6.5",
     "commander": "^14.0.3",
-    "dotenv": "^17.3.1",
     "glob": "^13.0.3",
     "mime-types": "^3.0.2",
     "minimatch": "^10.2.0",
diff --git a/packages/cli/src/bin/mxbai.ts b/packages/cli/src/bin/mxbai.ts
index cfbcf59..87dea68 100644
--- a/packages/cli/src/bin/mxbai.ts
+++ b/packages/cli/src/bin/mxbai.ts
@@ -15,25 +15,19 @@ import { setupGlobalOptions } from "../utils/global-options";
 import { checkForUpdates } from "../utils/update-checker";
 
 // Find package.json relative to the compiled file location
-// In the published package, from bin/mxbai.js, package.json is one level up
+const VERSION_PATHS = [
+  join(__dirname, "..", "package.json"),
+  join(__dirname, "..", "..", "package.json"),
+];
 let version = "0.0.0";
-try {
-  // First try one level up (for published package)
-  const packageJsonPath = join(__dirname, "..", "package.json");
-  const packageJson = JSON.parse(readFileSync(packageJsonPath, "utf-8"));
-  version = packageJson.version;
-} catch (_error) {
+for (const pkgPath of VERSION_PATHS) {
   try {
-    // Fallback to two levels up (for development/build environment)
-    const packageJsonPath = join(__dirname, "..", "..", "package.json");
-    const packageJson = JSON.parse(readFileSync(packageJsonPath, "utf-8"));
-    version = packageJson.version;
-  } catch (_error2) {
-    // Final fallback if package.json is not found
-    console.warn(
-      "Warning: Could not read package.json for version information"
-    );
-  }
+    version = JSON.parse(readFileSync(pkgPath, "utf-8")).version;
+    break;
+  } catch {}
+}
+if (version === "0.0.0") {
+  console.warn("Warning: Could not read package.json for version information");
 }
 
 const program = new Command();
@@ -76,7 +70,7 @@ program.on("command:*", () => {
 // Parse arguments
 async function main() {
   try {
-    await checkForUpdates(version);
+    const updateCheck = checkForUpdates(version);
 
     // Show help if no arguments provided
     if (process.argv.length === 2) {
@@ -84,6 +78,11 @@ async function main() {
     }
 
     await program.parseAsync(process.argv);
+
+    const banner = await updateCheck;
+    if (banner) {
+      console.error(banner);
+    }
   } catch (error) {
     if (error instanceof Error) {
       console.error(chalk.red("\n✗"), error.message);
diff --git a/packages/cli/src/commands/completion.ts b/packages/cli/src/commands/completion.ts
index d0b4202..91b69b9 100644
--- a/packages/cli/src/commands/completion.ts
+++ b/packages/cli/src/commands/completion.ts
@@ -1,10 +1,9 @@
 import path from "node:path";
-import { log as clackLog, spinner } from "@clack/prompts";
 import {
   getShellFromEnv,
   install,
-  log,
   parseEnv,
+  log as tabtabLog,
   uninstall,
 } from "@pnpm/tabtab";
 import chalk from "chalk";
@@ -17,10 +16,9 @@ import {
 import {
   addGlobalOptions,
   BaseGlobalOptionsSchema,
-  type GlobalOptions,
-  mergeCommandOptions,
   parseOptions,
 } from "../utils/global-options";
+import { log, spinner } from "../utils/logger";
 
 const SUPPORTED_SHELLS = ["bash", "zsh", "fish", "pwsh"] as const;
 export type SupportedShell = (typeof SUPPORTED_SHELLS)[number];
@@ -141,6 +139,7 @@ export function createCompletionCommand(): Command {
         }
       } catch (error) {
         console.error(chalk.red("✗"), "Error installing completion:", error);
+        process.exit(1);
       }
     });
 
@@ -158,6 +157,7 @@ export function createCompletionCommand(): Command {
         );
       } catch (error) {
         console.error(chalk.red("✗"), "Error uninstalling completion:", error);
+        process.exit(1);
       }
     });
 
@@ -167,8 +167,8 @@ export function createCompletionCommand(): Command {
     )
   );
 
-  refreshCommand.action(async (options: GlobalOptions) => {
-    const mergedOptions = mergeCommandOptions(refreshCommand, options);
+  refreshCommand.action(async () => {
+    const mergedOptions = refreshCommand.optsWithGlobals();
     const parsedOptions = parseOptions(BaseGlobalOptionsSchema, {
       ...mergedOptions,
     });
@@ -180,11 +180,12 @@ export function createCompletionCommand(): Command {
       refreshSpinner.stop("Completion cache refreshed successfully");
     } catch (error) {
       refreshSpinner.stop();
-      clackLog.error(
+      log.error(
         error instanceof Error
           ? error.message
           : "Failed to refresh completion cache"
       );
+      process.exit(1);
     }
   });
 
@@ -215,7 +216,7 @@ export function createCompletionServerCommand(): Command {
 
       // Root level completions - "mxbai " (when no previous command)
       if (env.words === 1) {
-        return log(
+        return tabtabLog(
           ["config", "store", "completion", "--help", "--version"],
           shell,
           console.log
@@ -241,7 +242,7 @@ export function createCompletionServerCommand(): Command {
           if (keyName) {
             const stores = getStoresForCompletion(keyName);
             if (stores.length > 0) {
-              return log(stores, shell, console.log);
+              return tabtabLog(stores, shell, console.log);
             }
           }
         }
@@ -249,7 +250,7 @@ export function createCompletionServerCommand(): Command {
 
       // Store completions
       if (env.prev === "store") {
-        return log(
+        return tabtabLog(
           [
             "create",
             "delete",
@@ -272,7 +273,7 @@ export function createCompletionServerCommand(): Command {
         // Check if we're in "mxbai store files " context
         const words = env.line.trim().split(/\s+/);
         if (words.length >= 3 && words[1] === "store") {
-          return log(["list", "get", "delete"], shell, console.log);
+          return tabtabLog(["list", "get", "delete"], shell, console.log);
         }
       }
 
@@ -291,7 +292,7 @@ export function createCompletionServerCommand(): Command {
           if (keyName) {
             const stores = getStoresForCompletion(keyName);
             if (stores.length > 0) {
-              return log(stores, shell, console.log);
+              return tabtabLog(stores, shell, console.log);
             }
           }
         }
@@ -299,14 +300,14 @@ export function createCompletionServerCommand(): Command {
 
       // Config completions
       if (env.prev === "config") {
-        return log(["get", "set", "keys"], shell, console.log);
+        return tabtabLog(["get", "set", "keys"], shell, console.log);
       }
 
       if (env.prev === "keys") {
         // Check if we're in "mxbai config keys " context
         const words = env.line.trim().split(/\s+/);
         if (words.length >= 3 && words[1] === "config") {
-          return log(
+          return tabtabLog(
             ["list", "add", "remove", "set-default"],
             shell,
             console.log
@@ -316,7 +317,11 @@ export function createCompletionServerCommand(): Command {
 
       // Completion completions
       if (env.prev === "completion") {
-        return log(["install", "uninstall", "refresh"], shell, console.log);
+        return tabtabLog(
+          ["install", "uninstall", "refresh"],
+          shell,
+          console.log
+        );
       }
     });
 
diff --git a/packages/cli/src/commands/config/keys.ts b/packages/cli/src/commands/config/keys.ts
index 5c3ce2f..10d07d3 100644
--- a/packages/cli/src/commands/config/keys.ts
+++ b/packages/cli/src/commands/config/keys.ts
@@ -1,4 +1,4 @@
-import { cancel, confirm, isCancel, log, text } from "@clack/prompts";
+import { cancel, confirm, isCancel, text } from "@clack/prompts";
 import chalk from "chalk";
 import { Command } from "commander";
 import { z } from "zod";
@@ -16,10 +16,9 @@ import {
 import {
   addGlobalOptions,
   BaseGlobalOptionsSchema,
-  type GlobalOptions,
-  mergeCommandOptions,
   parseOptions,
 } from "../../utils/global-options";
+import { log } from "../../utils/logger";
 
 const RemoveKeySchema = z.object({
   name: z.string().min(1, { error: '"name" is required' }),
@@ -34,8 +33,8 @@ export function createKeysCommand(): Command {
   keysCommand
     .command("add <key> [name]")
     .description("Add a new API key")
-    .action(async (key: string, name?: string, options?: GlobalOptions) => {
-      const mergedOptions = mergeCommandOptions(keysCommand, options);
+    .action(async (key: string, name?: string) => {
+      const mergedOptions = keysCommand.optsWithGlobals();
       const parsedOptions = parseOptions(BaseGlobalOptionsSchema, {
         ...mergedOptions,
       });
@@ -185,8 +184,8 @@ export function createKeysCommand(): Command {
   keysCommand
     .command("set-default <name>")
     .description("Set the default API key")
-    .action(async (name: string, options: GlobalOptions) => {
-      const mergedOptions = mergeCommandOptions(keysCommand, options);
+    .action(async (name: string) => {
+      const mergedOptions = keysCommand.optsWithGlobals();
       const parsedOptions = parseOptions(BaseGlobalOptionsSchema, {
         ...mergedOptions,
       });
diff --git a/packages/cli/src/commands/store/create.ts b/packages/cli/src/commands/store/create.ts
index e0113ba..bdffa2c 100644
--- a/packages/cli/src/commands/store/create.ts
+++ b/packages/cli/src/commands/store/create.ts
@@ -1,4 +1,3 @@
-import { log, spinner } from "@clack/prompts";
 import { Command } from "commander";
 import { z } from "zod";
 import { createClient } from "../../utils/client";
@@ -9,10 +8,9 @@ import {
 import {
   addGlobalOptions,
   extendGlobalOptions,
-  type GlobalOptions,
-  mergeCommandOptions,
   parseOptions,
 } from "../../utils/global-options";
+import { log, spinner } from "../../utils/logger";
 import { validateMetadata } from "../../utils/metadata";
 import { formatOutput } from "../../utils/output";
 import { buildStoreConfig, parsePublicFlag } from "../../utils/store";
@@ -30,14 +28,6 @@ const CreateStoreSchema = extendGlobalOptions({
   metadata: z.string().optional(),
 });
 
-interface CreateOptions extends GlobalOptions {
-  description?: string;
-  public?: boolean | string;
-  contextualization?: boolean | string;
-  expiresAfter?: number;
-  metadata?: string;
-}
-
 export function createCreateCommand(): Command {
   const command = addGlobalOptions(
     new Command("create")
@@ -56,11 +46,11 @@ export function createCreateCommand(): Command {
       .option("--metadata <json>", "Additional metadata as JSON string")
   );
 
-  command.action(async (name: string, options: CreateOptions) => {
+  command.action(async (name: string) => {
     const createSpinner = spinner();
 
     try {
-      const mergedOptions = mergeCommandOptions(command, options);
+      const mergedOptions = command.optsWithGlobals();
       const client = createClient(mergedOptions);
 
       const parsedOptions = parseOptions(CreateStoreSchema, {
diff --git a/packages/cli/src/commands/store/delete.ts b/packages/cli/src/commands/store/delete.ts
index 4f5e992..b436169 100644
--- a/packages/cli/src/commands/store/delete.ts
+++ b/packages/cli/src/commands/store/delete.ts
@@ -1,4 +1,4 @@
-import { confirm, isCancel, log, spinner } from "@clack/prompts";
+import { confirm, isCancel } from "@clack/prompts";
 import { Command } from "commander";
 import { z } from "zod";
 import { createClient } from "../../utils/client";
@@ -9,10 +9,9 @@ import {
 import {
   addGlobalOptions,
   extendGlobalOptions,
-  type GlobalOptions,
-  mergeCommandOptions,
   parseOptions,
 } from "../../utils/global-options";
+import { log, spinner } from "../../utils/logger";
 import { resolveStore } from "../../utils/store";
 
 const DeleteStoreSchema = extendGlobalOptions({
@@ -20,10 +19,6 @@ const DeleteStoreSchema = extendGlobalOptions({
   yes: z.boolean().optional(),
 });
 
-interface DeleteOptions extends GlobalOptions {
-  yes?: boolean;
-}
-
 export function createDeleteCommand(): Command {
   const command = addGlobalOptions(
     new Command("delete")
@@ -33,11 +28,10 @@ export function createDeleteCommand(): Command {
       .option("-y, --yes", "Skip confirmation prompt")
   );
 
-  command.action(async (nameOrId: string, options: DeleteOptions) => {
+  command.action(async (nameOrId: string) => {
     const deleteSpinner = spinner();
-
     try {
-      const mergedOptions = mergeCommandOptions(command, options);
+      const mergedOptions = command.optsWithGlobals();
 
       const parsedOptions = parseOptions(DeleteStoreSchema, {
         ...mergedOptions,
diff --git a/packages/cli/src/commands/store/files/delete.ts b/packages/cli/src/commands/store/files/delete.ts
index 074a51d..5b5799a 100644
--- a/packages/cli/src/commands/store/files/delete.ts
+++ b/packages/cli/src/commands/store/files/delete.ts
@@ -1,14 +1,13 @@
-import { confirm, isCancel, log, spinner } from "@clack/prompts";
+import { confirm, isCancel } from "@clack/prompts";
 import { Command } from "commander";
 import z from "zod";
 import { createClient } from "../../../utils/client";
 import {
   addGlobalOptions,
   extendGlobalOptions,
-  type GlobalOptions,
-  mergeCommandOptions,
   parseOptions,
 } from "../../../utils/global-options";
+import { log, spinner } from "../../../utils/logger";
 import { resolveStore } from "../../../utils/store";
 
 const DeleteFileSchema = extendGlobalOptions({
@@ -27,50 +26,49 @@ export function createDeleteCommand(): Command {
       .option("-y, --yes", "Skip confirmation prompt")
   );
 
-  deleteCommand.action(
-    async (nameOrId: string, fileId: string, options: GlobalOptions) => {
-      const deleteSpinner = spinner();
-      try {
-        const mergedOptions = mergeCommandOptions(deleteCommand, options);
+  deleteCommand.action(async (nameOrId: string, fileId: string) => {
+    const deleteSpinner = spinner();
 
-        const parsedOptions = parseOptions(DeleteFileSchema, {
-          ...mergedOptions,
-          nameOrId,
-          fileId,
-        });
+    try {
+      const mergedOptions = deleteCommand.optsWithGlobals();
+
+      const parsedOptions = parseOptions(DeleteFileSchema, {
+        ...mergedOptions,
+        nameOrId,
+        fileId,
+      });
 
-        const client = createClient(parsedOptions);
-        const store = await resolveStore(client, parsedOptions.nameOrId);
+      const client = createClient(parsedOptions);
+      const store = await resolveStore(client, parsedOptions.nameOrId);
 
-        // Confirmation prompt unless --yes is used
-        if (!parsedOptions.yes) {
-          const confirmed = await confirm({
-            message: `Are you sure you want to delete file "${parsedOptions.fileId}" from store "${store.name}" (${store.id})? This action cannot be undone.`,
-            initialValue: false,
-          });
+      // Confirmation prompt unless --yes is used
+      if (!parsedOptions.yes) {
+        const confirmed = await confirm({
+          message: `Are you sure you want to delete file "${parsedOptions.fileId}" from store "${store.name}" (${store.id})? This action cannot be undone.`,
+          initialValue: false,
+        });
 
-          if (isCancel(confirmed) || !confirmed) {
-            log.warn("Deletion cancelled.");
-            return;
-          }
+        if (isCancel(confirmed) || !confirmed) {
+          log.warn("Deletion cancelled.");
+          return;
         }
+      }
 
-        deleteSpinner.start("Deleting file...");
+      deleteSpinner.start("Deleting file...");
 
-        await client.stores.files.delete(parsedOptions.fileId, {
-          store_identifier: store.id,
-        });
+      await client.stores.files.delete(parsedOptions.fileId, {
+        store_identifier: store.id,
+      });
 
-        deleteSpinner.stop(`File ${parsedOptions.fileId} deleted successfully`);
-      } catch (error) {
-        deleteSpinner.stop();
-        log.error(
-          error instanceof Error ? error.message : "Failed to delete file"
-        );
-        process.exit(1);
-      }
+      deleteSpinner.stop(`File ${parsedOptions.fileId} deleted successfully`);
+    } catch (error) {
+      deleteSpinner.stop();
+      log.error(
+        error instanceof Error ? error.message : "Failed to delete file"
+      );
+      process.exit(1);
     }
-  );
+  });
 
   return deleteCommand;
 }
diff --git a/packages/cli/src/commands/store/files/get.ts b/packages/cli/src/commands/store/files/get.ts
index 258e4a2..2b48fba 100644
--- a/packages/cli/src/commands/store/files/get.ts
+++ b/packages/cli/src/commands/store/files/get.ts
@@ -1,14 +1,12 @@
-import { log, spinner } from "@clack/prompts";
 import { Command } from "commander";
 import { z } from "zod";
 import { createClient } from "../../../utils/client";
 import {
   addGlobalOptions,
   extendGlobalOptions,
-  type GlobalOptions,
-  mergeCommandOptions,
   parseOptions,
 } from "../../../utils/global-options";
+import { log, spinner } from "../../../utils/logger";
 import { formatBytes, formatOutput } from "../../../utils/output";
 import { resolveStore } from "../../../utils/store";
 
@@ -25,51 +23,49 @@ export function createGetCommand(): Command {
       .argument("<file-id>", "ID of the file")
   );
 
-  getCommand.action(
-    async (nameOrId: string, fileId: string, options: GlobalOptions) => {
-      const getSpinner = spinner();
+  getCommand.action(async (nameOrId: string, fileId: string) => {
+    const getSpinner = spinner();
 
-      try {
-        const mergedOptions = mergeCommandOptions(getCommand, options);
+    try {
+      const mergedOptions = getCommand.optsWithGlobals();
 
-        const parsedOptions = parseOptions(GetFileSchema, {
-          ...mergedOptions,
-          nameOrId,
-          fileId,
-        });
+      const parsedOptions = parseOptions(GetFileSchema, {
+        ...mergedOptions,
+        nameOrId,
+        fileId,
+      });
 
-        const client = createClient(parsedOptions);
-        getSpinner.start("Loading file details...");
-        const store = await resolveStore(client, parsedOptions.nameOrId);
+      const client = createClient(parsedOptions);
+      getSpinner.start("Loading file details...");
+      const store = await resolveStore(client, parsedOptions.nameOrId);
 
-        const file = await client.stores.files.retrieve(parsedOptions.fileId, {
-          store_identifier: store.id,
-        });
+      const file = await client.stores.files.retrieve(parsedOptions.fileId, {
+        store_identifier: store.id,
+      });
 
-        getSpinner.stop("File details loaded");
+      getSpinner.stop("File details loaded");
 
-        const formattedData = {
-          id: file.id,
-          name: file.filename,
-          status: file.status,
-          size: formatBytes(file.usage_bytes),
-          "created at": new Date(file.created_at).toLocaleString(),
-          metadata:
-            parsedOptions.format === "table"
-              ? JSON.stringify(file.metadata, null, 2)
-              : file.metadata,
-        };
+      const formattedData = {
+        id: file.id,
+        name: file.filename,
+        status: file.status,
+        size: formatBytes(file.usage_bytes),
+        "created at": new Date(file.created_at).toLocaleString(),
+        metadata:
+          parsedOptions.format === "table"
+            ? JSON.stringify(file.metadata, null, 2)
+            : file.metadata,
+      };
 
-        formatOutput(formattedData, parsedOptions.format);
-      } catch (error) {
-        getSpinner.stop();
-        log.error(
-          error instanceof Error ? error.message : "Failed to get file details"
-        );
-        process.exit(1);
-      }
+      formatOutput(formattedData, parsedOptions.format);
+    } catch (error) {
+      getSpinner.stop();
+      log.error(
+        error instanceof Error ? error.message : "Failed to get file details"
+      );
+      process.exit(1);
     }
-  );
+  });
 
   return getCommand;
 }
diff --git a/packages/cli/src/commands/store/files/list.ts b/packages/cli/src/commands/store/files/list.ts
index 951c751..93319a0 100644
--- a/packages/cli/src/commands/store/files/list.ts
+++ b/packages/cli/src/commands/store/files/list.ts
@@ -1,4 +1,3 @@
-import { log, spinner } from "@clack/prompts";
 import type { StoreFile } from "@mixedbread/sdk/resources/stores";
 import { Command } from "commander";
 import { z } from "zod";
@@ -6,16 +5,15 @@ import { createClient } from "../../../utils/client";
 import {
   addGlobalOptions,
   extendGlobalOptions,
-  mergeCommandOptions,
   parseOptions,
 } from "../../../utils/global-options";
+import { log, spinner } from "../../../utils/logger";
 import {
   formatBytes,
   formatCountWithSuffix,
   formatOutput,
 } from "../../../utils/output";
 import { resolveStore } from "../../../utils/store";
-import type { FilesOptions } from ".";
 
 const ListFilesSchema = extendGlobalOptions({
   nameOrId: z.string().min(1, { error: '"name-or-id" is required' }),
@@ -46,11 +44,11 @@ export function createListCommand(): Command {
       .option("--limit <n>", "Maximum number of results", "10")
   );
 
-  listCommand.action(async (nameOrId: string, options: FilesOptions) => {
+  listCommand.action(async (nameOrId: string) => {
     const listSpinner = spinner();
 
     try {
-      const mergedOptions = mergeCommandOptions(listCommand, options);
+      const mergedOptions = listCommand.optsWithGlobals();
       const parsedOptions = parseOptions(ListFilesSchema, {
         ...mergedOptions,
         nameOrId,
diff --git a/packages/cli/src/commands/store/get.ts b/packages/cli/src/commands/store/get.ts
index 834ac47..6c35ece 100644
--- a/packages/cli/src/commands/store/get.ts
+++ b/packages/cli/src/commands/store/get.ts
@@ -1,14 +1,12 @@
-import { log, spinner } from "@clack/prompts";
 import { Command } from "commander";
 import { z } from "zod";
 import { createClient } from "../../utils/client";
 import {
   addGlobalOptions,
   extendGlobalOptions,
-  type GlobalOptions,
-  mergeCommandOptions,
   parseOptions,
 } from "../../utils/global-options";
+import { log, spinner } from "../../utils/logger";
 import { formatBytes, formatOutput } from "../../utils/output";
 import { resolveStore } from "../../utils/store";
 
@@ -16,8 +14,6 @@ const GetStoreSchema = extendGlobalOptions({
   nameOrId: z.string().min(1, { error: '"name-or-id" is required' }),
 });
 
-interface GetOptions extends GlobalOptions {}
-
 export function createGetCommand(): Command {
   const command = addGlobalOptions(
     new Command("get")
@@ -25,11 +21,11 @@ export function createGetCommand(): Command {
       .argument("<name-or-id>", "Name or ID of the store")
   );
 
-  command.action(async (nameOrId: string, options: GetOptions) => {
+  command.action(async (nameOrId: string) => {
     const getSpinner = spinner();
 
     try {
-      const mergedOptions = mergeCommandOptions(command, options);
+      const mergedOptions = command.optsWithGlobals();
 
       const parsedOptions = parseOptions(GetStoreSchema, {
         ...mergedOptions,
diff --git a/packages/cli/src/commands/store/list.ts b/packages/cli/src/commands/store/list.ts
index 9b5b836..5557bb8 100644
--- a/packages/cli/src/commands/store/list.ts
+++ b/packages/cli/src/commands/store/list.ts
@@ -1,4 +1,3 @@
-import { log, spinner } from "@clack/prompts";
 import { Command } from "commander";
 import { z } from "zod";
 import { createClient } from "../../utils/client";
@@ -9,10 +8,9 @@ import {
 import {
   addGlobalOptions,
   extendGlobalOptions,
-  type GlobalOptions,
-  mergeCommandOptions,
   parseOptions,
 } from "../../utils/global-options";
+import { log, spinner } from "../../utils/logger";
 import {
   formatBytes,
   formatCountWithSuffix,
@@ -29,11 +27,6 @@ const ListStoreSchema = extendGlobalOptions({
     .optional(),
 });
 
-interface ListOptions extends GlobalOptions {
-  filter?: string;
-  limit?: number;
-}
-
 export function createListCommand(): Command {
   const command = addGlobalOptions(
     new Command("list")
@@ -42,11 +35,11 @@ export function createListCommand(): Command {
       .option("--limit <n>", "Maximum number of results", "100")
   );
 
-  command.action(async (options: ListOptions) => {
+  command.action(async () => {
     const listSpinner = spinner();
 
     try {
-      const mergedOptions = mergeCommandOptions(command, options);
+      const mergedOptions = command.optsWithGlobals();
       const parsedOptions = parseOptions(
         ListStoreSchema,
         mergedOptions as Record<string, unknown>
@@ -87,7 +80,9 @@ export function createListCommand(): Command {
         created: new Date(store.created_at).toLocaleDateString(),
       }));
 
-      listSpinner.stop(`Found ${formatCountWithSuffix(stores.length, "store")}`);
+      listSpinner.stop(
+        `Found ${formatCountWithSuffix(stores.length, "store")}`
+      );
       formatOutput(formattedData, parsedOptions.format);
 
       // Update completion cache with the fetched stores
diff --git a/packages/cli/src/commands/store/qa.ts b/packages/cli/src/commands/store/qa.ts
index 3e8582c..1660c13 100644
--- a/packages/cli/src/commands/store/qa.ts
+++ b/packages/cli/src/commands/store/qa.ts
@@ -1,4 +1,3 @@
-import { log, spinner } from "@clack/prompts";
 import chalk from "chalk";
 import { Command } from "commander";
 import { z } from "zod";
@@ -7,10 +6,9 @@ import { loadConfig } from "../../utils/config";
 import {
   addGlobalOptions,
   extendGlobalOptions,
-  type GlobalOptions,
-  mergeCommandOptions,
   parseOptions,
 } from "../../utils/global-options";
+import { log, spinner } from "../../utils/logger";
 import { formatOutput } from "../../utils/output";
 import { resolveStore } from "../../utils/store";
 
@@ -33,14 +31,6 @@ const QAStoreSchema = extendGlobalOptions({
   returnMetadata: z.boolean().optional(),
 });
 
-interface QAOptions extends GlobalOptions {
-  topK?: number;
-  threshold?: number;
-  cite?: boolean;
-  multimodal?: boolean;
-  returnMetadata?: boolean;
-}
-
 export function createQACommand(): Command {
   const command = addGlobalOptions(
     new Command("qa")
@@ -52,80 +42,78 @@ export function createQACommand(): Command {
       .option("--return-metadata", "Return source metadata")
   );
 
-  command.action(
-    async (nameOrId: string, question: string, options: QAOptions) => {
-      const qaSpinner = spinner();
-
-      try {
-        const mergedOptions = mergeCommandOptions(command, options);
-        const parsedOptions = parseOptions(QAStoreSchema, {
-          ...mergedOptions,
-          nameOrId,
-          question,
+  command.action(async (nameOrId: string, question: string) => {
+    const qaSpinner = spinner();
+
+    try {
+      const mergedOptions = command.optsWithGlobals();
+      const parsedOptions = parseOptions(QAStoreSchema, {
+        ...mergedOptions,
+        nameOrId,
+        question,
+      });
+
+      const client = createClient(parsedOptions);
+      qaSpinner.start("Processing question...");
+      const store = await resolveStore(client, parsedOptions.nameOrId);
+      const config = loadConfig();
+
+      // Get default values from config
+      const topK = parsedOptions.topK || config.defaults?.search?.top_k || 10;
+
+      const response = await client.stores.questionAnswering({
+        query: parsedOptions.question,
+        store_identifiers: [store.id],
+        top_k: topK,
+        search_options: {
+          score_threshold: parsedOptions.threshold
+            ? parsedOptions.threshold
+            : undefined,
+          return_metadata: parsedOptions.returnMetadata
+            ? parsedOptions.returnMetadata
+            : undefined,
+        },
+      });
+
+      qaSpinner.stop("Question processed");
+
+      // Display the answer
+      console.log(chalk.bold(chalk.blue("\nAnswer:")));
+      console.log(response.answer);
+
+      // Display sources if available
+      if (response.sources && response.sources.length > 0) {
+        console.log(chalk.bold(chalk.blue("\nSources:")));
+
+        const sources = response.sources.map((source) => {
+          const metadata =
+            parsedOptions.format === "table"
+              ? JSON.stringify(source.metadata, null, 2)
+              : source.metadata;
+
+          const output: Record<string, unknown> = {
+            filename: source.filename,
+            score: source.score.toFixed(2),
+            chunk_index: source.chunk_index,
+          };
+
+          if (parsedOptions.returnMetadata) {
+            output.metadata = metadata;
+          }
+
+          return output;
         });
 
-        const client = createClient(parsedOptions);
-        qaSpinner.start("Processing question...");
-        const store = await resolveStore(client, parsedOptions.nameOrId);
-        const config = loadConfig();
-
-        // Get default values from config
-        const topK = parsedOptions.topK || config.defaults?.search?.top_k || 10;
-
-        const response = await client.stores.questionAnswering({
-          query: parsedOptions.question,
-          store_identifiers: [store.id],
-          top_k: topK,
-          search_options: {
-            score_threshold: parsedOptions.threshold
-              ? parsedOptions.threshold
-              : undefined,
-            return_metadata: parsedOptions.returnMetadata
-              ? parsedOptions.returnMetadata
-              : undefined,
-          },
-        });
-
-        qaSpinner.stop("Question processed");
-
-        // Display the answer
-        console.log(chalk.bold(chalk.blue("\nAnswer:")));
-        console.log(response.answer);
-
-        // Display sources if available
-        if (response.sources && response.sources.length > 0) {
-          console.log(chalk.bold(chalk.blue("\nSources:")));
-
-          const sources = response.sources.map((source) => {
-            const metadata =
-              parsedOptions.format === "table"
-                ? JSON.stringify(source.metadata, null, 2)
-                : source.metadata;
-
-            const output: Record<string, unknown> = {
-              filename: source.filename,
-              score: source.score.toFixed(2),
-              chunk_index: source.chunk_index,
-            };
-
-            if (parsedOptions.returnMetadata) {
-              output.metadata = metadata;
-            }
-
-            return output;
-          });
-
-          formatOutput(sources, parsedOptions.format);
-        }
-      } catch (error) {
-        qaSpinner.stop();
-        log.error(
-          error instanceof Error ? error.message : "Failed to process question"
-        );
-        process.exit(1);
+        formatOutput(sources, parsedOptions.format);
       }
+    } catch (error) {
+      qaSpinner.stop();
+      log.error(
+        error instanceof Error ? error.message : "Failed to process question"
+      );
+      process.exit(1);
     }
-  );
+  });
 
   return command;
 }
diff --git a/packages/cli/src/commands/store/search.ts b/packages/cli/src/commands/store/search.ts
index be01031..f921b86 100644
--- a/packages/cli/src/commands/store/search.ts
+++ b/packages/cli/src/commands/store/search.ts
@@ -1,4 +1,3 @@
-import { log, spinner } from "@clack/prompts";
 import type Mixedbread from "@mixedbread/sdk";
 import { Command } from "commander";
 import { z } from "zod";
@@ -7,10 +6,9 @@ import { loadConfig } from "../../utils/config";
 import {
   addGlobalOptions,
   extendGlobalOptions,
-  type GlobalOptions,
-  mergeCommandOptions,
   parseOptions,
 } from "../../utils/global-options";
+import { log, spinner } from "../../utils/logger";
 import { formatCountWithSuffix, formatOutput } from "../../utils/output";
 import { resolveStore } from "../../utils/store";
 
@@ -69,14 +67,6 @@ async function searchStoreChunks(
   });
 }
 
-interface SearchOptions extends GlobalOptions {
-  topK?: number;
-  threshold?: number;
-  returnMetadata?: boolean;
-  rerank?: boolean;
-  fileSearch?: boolean;
-}
-
 export function createSearchCommand(): Command {
   const command = addGlobalOptions(
     new Command("search")
@@ -90,83 +80,83 @@ export function createSearchCommand(): Command {
       .option("--file-search", "Search files instead of chunks", false)
   );
 
-  command.action(
-    async (nameOrId: string, query: string, options: SearchOptions) => {
-      const searchSpinner = spinner();
-
-      try {
-        const mergedOptions = mergeCommandOptions(command, options);
-        const parsedOptions = parseOptions(SearchStoreSchema, {
-          ...mergedOptions,
-          nameOrId,
-          query,
-        });
-
-        const client = createClient(parsedOptions);
-        searchSpinner.start("Searching store...");
-        const store = await resolveStore(client, parsedOptions.nameOrId);
-        const config = loadConfig();
-
-        // Get default values from config
-        const topK = parsedOptions.topK || config.defaults?.search?.top_k || 10;
-        const rerank =
-          parsedOptions.rerank ?? config.defaults?.search?.rerank ?? false;
-
-        const results = parsedOptions.fileSearch
-          ? await searchStoreFiles(client, {
-              ...parsedOptions,
-              storeIdentifier: store.id,
-              topK,
-              rerank,
-            })
-          : await searchStoreChunks(client, {
-              ...parsedOptions,
-              storeIdentifier: store.id,
-              topK,
-              rerank,
-            });
-
-        if (!results.data || results.data.length === 0) {
-          searchSpinner.stop();
-          log.info("No results found.");
-          return;
-        }
+  command.action(async (nameOrId: string, query: string) => {
+    const searchSpinner = spinner();
+
+    try {
+      const mergedOptions = command.optsWithGlobals();
+      const parsedOptions = parseOptions(SearchStoreSchema, {
+        ...mergedOptions,
+        nameOrId,
+        query,
+      });
+
+      const client = createClient(parsedOptions);
+      searchSpinner.start("Searching store...");
+      const store = await resolveStore(client, parsedOptions.nameOrId);
+      const config = loadConfig();
+
+      // Get default values from config
+      const topK = parsedOptions.topK || config.defaults?.search?.top_k || 10;
+      const rerank =
+        parsedOptions.rerank ?? config.defaults?.search?.rerank ?? false;
+
+      const results = parsedOptions.fileSearch
+        ? await searchStoreFiles(client, {
+            ...parsedOptions,
+            storeIdentifier: store.id,
+            topK,
+            rerank,
+          })
+        : await searchStoreChunks(client, {
+            ...parsedOptions,
+            storeIdentifier: store.id,
+            topK,
+            rerank,
+          });
+
+      if (!results.data || results.data.length === 0) {
+        searchSpinner.stop();
+        log.info("No results found.");
+        return;
+      }
 
-        searchSpinner.stop(`Found ${formatCountWithSuffix(results.data.length, "result")}`);
+      searchSpinner.stop(
+        `Found ${formatCountWithSuffix(results.data.length, "result")}`
+      );
 
-        const output = results.data.map((result) => {
-          const metadata =
-            parsedOptions.format === "table"
-              ? JSON.stringify(result.metadata, null, 2)
-              : result.metadata;
+      const output = results.data.map((result) => {
+        const metadata =
+          parsedOptions.format === "table"
+            ? JSON.stringify(result.metadata, null, 2)
+            : result.metadata;
 
-          const output: Record<string, unknown> = {
-            filename: result.filename,
-            score: result.score.toFixed(2),
-            store_id: result.store_id,
-          };
+        const output: Record<string, unknown> = {
+          filename: result.filename,
+          score: result.score.toFixed(2),
+          store_id: result.store_id,
+        };
 
-          if (!parsedOptions.fileSearch) {
-            output.chunk_index = result.chunk_index;
-          }
+        if (!parsedOptions.fileSearch) {
+          output.chunk_index = result.chunk_index;
+        }
 
-          if (parsedOptions.returnMetadata) {
-            output.metadata = metadata;
-          }
+        if (parsedOptions.returnMetadata) {
+          output.metadata = metadata;
+        }
 
-          return output;
-        });
+        return output;
+      });
 
-        formatOutput(output, parsedOptions.format);
-      } catch (error) {
-        searchSpinner.stop();
-        log.error(
-          error instanceof Error ? error.message : "Failed to search store"
-        );
-        process.exit(1);
-      }
+      formatOutput(output, parsedOptions.format);
+    } catch (error) {
+      searchSpinner.stop();
+      log.error(
+        error instanceof Error ? error.message : "Failed to search store"
+      );
+      process.exit(1);
     }
-  );
+  });
 
   return command;
 }
diff --git a/packages/cli/src/commands/store/sync.ts b/packages/cli/src/commands/store/sync.ts
index b2fccf7..1375c75 100644
--- a/packages/cli/src/commands/store/sync.ts
+++ b/packages/cli/src/commands/store/sync.ts
@@ -1,5 +1,4 @@
-import { confirm, isCancel, log, spinner } from "@clack/prompts";
-import type { FileCreateParams } from "@mixedbread/sdk/resources/stores";
+import { confirm, isCancel } from "@clack/prompts";
 import chalk from "chalk";
 import { Command } from "commander";
 import { z } from "zod";
@@ -9,10 +8,9 @@ import { getGitInfo } from "../../utils/git";
 import {
   addGlobalOptions,
   extendGlobalOptions,
-  type GlobalOptions,
-  mergeCommandOptions,
   parseOptions,
 } from "../../utils/global-options";
+import { log, spinner } from "../../utils/logger";
 import { validateMetadata } from "../../utils/metadata";
 import { formatBytes, formatCountWithSuffix } from "../../utils/output";
 import { resolveStore } from "../../utils/store";
@@ -47,17 +45,6 @@ const SyncStoreSchema = extendGlobalOptions({
     .default(100),
 });
 
-interface SyncOptions extends GlobalOptions {
-  strategy?: FileCreateParams.Config["parsing_strategy"];
-  contextualization?: boolean;
-  fromGit?: string;
-  dryRun?: boolean;
-  yes?: boolean;
-  force?: boolean;
-  metadata?: string;
-  parallel?: number;
-}
-
 export function createSyncCommand(): Command {
   const command = addGlobalOptions(
     new Command("sync")
@@ -86,145 +73,143 @@ export function createSyncCommand(): Command {
       .option("--parallel <n>", "Number of concurrent operations (1-200)")
   );
 
-  command.action(
-    async (nameOrId: string, patterns: string[], options: SyncOptions) => {
-      try {
-        const mergedOptions = mergeCommandOptions(command, options);
-        const parsedOptions = parseOptions(SyncStoreSchema, {
-          ...mergedOptions,
-          nameOrId,
-          patterns,
-        });
+  command.action(async (nameOrId: string, patterns: string[]) => {
+    let activeSpinner: ReturnType<typeof spinner> | null = null;
+    try {
+      const mergedOptions = command.optsWithGlobals();
+      const parsedOptions = parseOptions(SyncStoreSchema, {
+        ...mergedOptions,
+        nameOrId,
+        patterns,
+      });
 
-        const client = createClient(parsedOptions);
+      const client = createClient(parsedOptions);
 
-        console.log(chalk.bold.blue("🔄 Starting Store Sync"));
+      console.log(chalk.bold.blue("🔄 Starting Store Sync"));
 
-        if (parsedOptions.contextualization) {
-          warnContextualizationDeprecated("store sync");
-        }
+      if (parsedOptions.contextualization) {
+        warnContextualizationDeprecated("store sync");
+      }
 
-        // Step 0: Resolve store
-        const resolveSpinner = spinner();
-        resolveSpinner.start(`Looking up store "${parsedOptions.nameOrId}"...`);
-        const store = await resolveStore(client, parsedOptions.nameOrId);
-        resolveSpinner.stop(`Found store: ${store.name}`);
+      // Step 0: Resolve store
+      activeSpinner = spinner();
+      activeSpinner.start(`Looking up store "${parsedOptions.nameOrId}"...`);
+      const store = await resolveStore(client, parsedOptions.nameOrId);
+      activeSpinner.stop(`Found store: ${store.name}`);
+      activeSpinner = null;
 
-        // Parse metadata if provided
-        const additionalMetadata = validateMetadata(parsedOptions.metadata);
+      // Parse metadata if provided
+      const additionalMetadata = validateMetadata(parsedOptions.metadata);
 
-        // Get git info
-        const gitInfo = await getGitInfo();
+      // Get git info
+      const gitInfo = await getGitInfo();
 
-        const loadSpinner = spinner();
-        loadSpinner.start("Loading existing files from store...");
+      activeSpinner = spinner();
+      activeSpinner.start("Loading existing files from store...");
 
-        const syncedFiles = await getSyncedFiles(client, store.id);
+      const syncedFiles = await getSyncedFiles(client, store.id);
 
-        loadSpinner.stop(
-          `Found ${formatCountWithSuffix(syncedFiles.size, "existing file")} in store`
-        );
+      activeSpinner.stop(
+        `Found ${formatCountWithSuffix(syncedFiles.size, "existing file")} in store`
+      );
+      activeSpinner = null;
 
-        const fromGit = parsedOptions.fromGit;
-
-        if (parsedOptions.force) {
-          log.success("Force upload enabled - all files will be re-uploaded");
-        } else if (fromGit && gitInfo.isRepo) {
-          log.success(
-            `Git-based detection enabled (from commit ${fromGit.substring(0, 7)})`
-          );
-        } else if (fromGit && !gitInfo.isRepo) {
-          log.error("--from-git specified but not in a git repository");
-          process.exit(1);
-        } else {
-          log.success("Hash-based detection enabled (comparing file contents)");
-        }
+      const fromGit = parsedOptions.fromGit;
 
-        const analyzeSpinner = spinner();
-        analyzeSpinner.start("Scanning files and detecting changes...");
-        const analysis = await analyzeChanges({
-          patterns,
-          syncedFiles,
-          gitInfo,
-          fromGit,
-          forceUpload: parsedOptions.force,
-        });
+      if (parsedOptions.force) {
+        log.success("Force upload enabled - all files will be re-uploaded");
+      } else if (fromGit && gitInfo.isRepo) {
+        log.success(
+          `Git-based detection enabled (from commit ${fromGit.substring(0, 7)})`
+        );
+      } else if (fromGit && !gitInfo.isRepo) {
+        log.error("--from-git specified but not in a git repository");
+        process.exit(1);
+      } else {
+        log.success("Hash-based detection enabled (comparing file contents)");
+      }
 
-        analyzeSpinner.stop("Change analysis complete");
+      activeSpinner = spinner();
+      activeSpinner.start("Scanning files and detecting changes...");
+      const analysis = await analyzeChanges({
+        patterns,
+        syncedFiles,
+        gitInfo,
+        fromGit,
+        forceUpload: parsedOptions.force,
+      });
+
+      activeSpinner.stop("Change analysis complete");
+      activeSpinner = null;
+
+      const totalChanges =
+        analysis.added.length +
+        analysis.modified.length +
+        analysis.deleted.length;
+
+      if (totalChanges === 0) {
+        log.success("Store is already in sync - no changes needed!");
+        return;
+      }
 
-        const totalChanges =
-          analysis.added.length +
-          analysis.modified.length +
-          analysis.deleted.length;
+      // Show summary
+      if (parsedOptions.force) {
+        console.log(chalk.bold("\n--force enabled"));
+        console.log(
+          `All ${formatCountWithSuffix(analysis.totalFiles, "file")} will be re-uploaded to the store.`
+        );
+        console.log(`Upload size: ${formatBytes(analysis.totalSize)}\n`);
+      } else {
+        console.log(`${formatChangeSummary(analysis)}\n`);
+      }
 
-        if (totalChanges === 0) {
-          log.success("Store is already in sync - no changes needed!");
-          return;
-        }
+      // Dry run mode - just show what would happen
+      if (parsedOptions.dryRun) {
+        console.log(chalk.yellow.bold("Dry Run Complete"));
+        console.log(
+          chalk.yellow(
+            "No changes were made - this was a preview of what would happen."
+          )
+        );
+        return;
+      }
 
-        // Show summary
-        if (parsedOptions.force) {
-          console.log(chalk.bold("\n--force enabled"));
-          console.log(
-            `All ${formatCountWithSuffix(analysis.totalFiles, "file")} will be re-uploaded to the store.`
-          );
-          console.log(`Upload size: ${formatBytes(analysis.totalSize)}\n`);
-        } else {
-          console.log(`${formatChangeSummary(analysis)}\n`);
-        }
+      // Confirm changes unless yes flag is set
+      if (!parsedOptions.yes) {
+        const proceed = await confirm({
+          message: "Apply these changes to the store?",
+        });
 
-        // Dry run mode - just show what would happen
-        if (parsedOptions.dryRun) {
-          console.log(chalk.yellow.bold("Dry Run Complete"));
-          console.log(
-            chalk.yellow(
-              "No changes were made - this was a preview of what would happen."
-            )
-          );
+        if (isCancel(proceed) || !proceed) {
+          log.warn("Sync cancelled by user");
           return;
         }
+      } else if (parsedOptions.yes) {
+        log.success("Auto-proceeding with --yes flag");
+      }
 
-        // Confirm changes unless yes flag is set
-        if (!parsedOptions.yes) {
-          const proceed = await confirm({
-            message: "Apply these changes to the store?",
-          });
-
-          if (isCancel(proceed) || !proceed) {
-            log.warn("Sync cancelled by user");
-            return;
-          }
-        } else if (parsedOptions.yes) {
-          log.success("Auto-proceeding with --yes flag");
-        }
-
-        // Execute changes
-        const syncResults = await executeSyncChanges(
-          client,
-          store.id,
-          analysis,
-          {
-            strategy: parsedOptions.strategy,
-            metadata: additionalMetadata,
-            gitInfo: gitInfo.isRepo ? gitInfo : undefined,
-            parallel: parsedOptions.parallel,
-          }
-        );
-
-        // Display summary
-        displaySyncResultsSummary(syncResults, gitInfo, fromGit, {
-          strategy: parsedOptions.strategy,
-        });
-      } catch (error) {
-        if (error instanceof Error) {
-          log.error(error.message);
-        } else {
-          log.error("Failed to sync store");
-        }
-        process.exit(1);
+      // Execute changes
+      const syncResults = await executeSyncChanges(client, store.id, analysis, {
+        strategy: parsedOptions.strategy,
+        metadata: additionalMetadata,
+        gitInfo: gitInfo.isRepo ? gitInfo : undefined,
+        parallel: parsedOptions.parallel,
+      });
+
+      // Display summary
+      displaySyncResultsSummary(syncResults, gitInfo, fromGit, {
+        strategy: parsedOptions.strategy,
+      });
+    } catch (error) {
+      activeSpinner?.stop();
+      if (error instanceof Error) {
+        log.error(error.message);
+      } else {
+        log.error("Failed to sync store");
       }
+      process.exit(1);
     }
-  );
+  });
 
   return command;
 }
diff --git a/packages/cli/src/commands/store/update.ts b/packages/cli/src/commands/store/update.ts
index 6d67ca3..f81724c 100644
--- a/packages/cli/src/commands/store/update.ts
+++ b/packages/cli/src/commands/store/update.ts
@@ -1,4 +1,3 @@
-import { log, spinner } from "@clack/prompts";
 import type { StoreUpdateParams } from "@mixedbread/sdk/resources/index";
 import { Command } from "commander";
 import { z } from "zod";
@@ -10,10 +9,9 @@ import {
 import {
   addGlobalOptions,
   extendGlobalOptions,
-  type GlobalOptions,
-  mergeCommandOptions,
   parseOptions,
 } from "../../utils/global-options";
+import { log, spinner } from "../../utils/logger";
 import { validateMetadata } from "../../utils/metadata";
 import { formatOutput } from "../../utils/output";
 import { parsePublicFlag, resolveStore } from "../../utils/store";
@@ -31,14 +29,6 @@ const UpdateStoreSchema = extendGlobalOptions({
   metadata: z.string().optional(),
 });
 
-interface UpdateOptions extends GlobalOptions {
-  name?: string;
-  description?: string;
-  public?: boolean | string;
-  expiresAfter?: number;
-  metadata?: string;
-}
-
 export function createUpdateCommand(): Command {
   const command = addGlobalOptions(
     new Command("update")
@@ -57,11 +47,11 @@ export function createUpdateCommand(): Command {
       )
   );
 
-  command.action(async (nameOrId: string, options: UpdateOptions) => {
+  command.action(async (nameOrId: string) => {
     const updateSpinner = spinner();
 
     try {
-      const mergedOptions = mergeCommandOptions(command, options);
+      const mergedOptions = command.optsWithGlobals();
 
       const parsedOptions = parseOptions(UpdateStoreSchema, {
         ...mergedOptions,
diff --git a/packages/cli/src/commands/store/upload.ts b/packages/cli/src/commands/store/upload.ts
index c139dc5..b9d0daf 100644
--- a/packages/cli/src/commands/store/upload.ts
+++ b/packages/cli/src/commands/store/upload.ts
@@ -1,5 +1,4 @@
-import { statSync } from "node:fs";
-import { log, spinner } from "@clack/prompts";
+import { stat } from "node:fs/promises";
 import type { FileCreateParams } from "@mixedbread/sdk/resources/stores";
 import chalk from "chalk";
 import { Command } from "commander";
@@ -12,13 +11,13 @@ import {
   addGlobalOptions,
   extendGlobalOptions,
   type GlobalOptions,
-  mergeCommandOptions,
   parseOptions,
 } from "../../utils/global-options";
+import { log, spinner } from "../../utils/logger";
 import { uploadFromManifest } from "../../utils/manifest";
 import { validateMetadata } from "../../utils/metadata";
 import { formatBytes, formatCountWithSuffix } from "../../utils/output";
-import { getStoreFiles, resolveStore } from "../../utils/store";
+import { checkExistingFiles, resolveStore } from "../../utils/store";
 import { type FileToUpload, uploadFilesInBatch } from "../../utils/upload";
 
 const UploadStoreSchema = extendGlobalOptions({
@@ -45,7 +44,7 @@ const UploadStoreSchema = extendGlobalOptions({
 });
 
 export interface UploadOptions extends GlobalOptions {
-  strategy?: FileCreateParams.Experimental["parsing_strategy"];
+  strategy?: FileCreateParams.Config["parsing_strategy"];
   contextualization?: boolean;
   metadata?: string;
   dryRun?: boolean;
@@ -79,161 +78,151 @@ export function createUploadCommand(): Command {
       .option("--manifest <file>", "Upload using manifest file")
   );
 
-  command.action(
-    async (nameOrId: string, patterns: string[], options: UploadOptions) => {
-      try {
-        const mergedOptions = mergeCommandOptions(command, options);
+  command.action(async (nameOrId: string, patterns: string[]) => {
+    let activeSpinner: ReturnType<typeof spinner> | null = null;
+    try {
+      const mergedOptions = command.optsWithGlobals();
 
-        const parsedOptions = parseOptions(UploadStoreSchema, {
-          ...mergedOptions,
-          nameOrId,
-          patterns,
-        });
-
-        if (parsedOptions.contextualization) {
-          warnContextualizationDeprecated("store upload");
-        }
+      const parsedOptions = parseOptions(UploadStoreSchema, {
+        ...mergedOptions,
+        nameOrId,
+        patterns,
+      });
 
-        const client = createClient(parsedOptions);
-        const initializeSpinner = spinner();
-        initializeSpinner.start("Initializing upload...");
-        const store = await resolveStore(client, parsedOptions.nameOrId);
-        const config = loadConfig();
+      if (parsedOptions.contextualization) {
+        warnContextualizationDeprecated("store upload");
+      }
 
-        initializeSpinner.stop("Upload initialized");
+      const client = createClient(parsedOptions);
+      activeSpinner = spinner();
+      activeSpinner.start("Initializing upload...");
+      const store = await resolveStore(client, parsedOptions.nameOrId);
+      const config = loadConfig();
+
+      activeSpinner.stop("Upload initialized");
+      activeSpinner = null;
+
+      // Handle manifest file upload
+      if (parsedOptions.manifest) {
+        return await uploadFromManifest(
+          client,
+          store.id,
+          parsedOptions.manifest,
+          parsedOptions
+        );
+      }
 
-        // Handle manifest file upload
-        if (parsedOptions.manifest) {
-          return await uploadFromManifest(
-            client,
-            store.id,
-            parsedOptions.manifest,
-            parsedOptions
-          );
-        }
+      if (!parsedOptions.patterns || parsedOptions.patterns.length === 0) {
+        log.error(
+          "No file patterns provided. Use --manifest for manifest-based uploads."
+        );
+        process.exit(1);
+      }
 
-        if (!parsedOptions.patterns || parsedOptions.patterns.length === 0) {
-          log.error(
-            "No file patterns provided. Use --manifest for manifest-based uploads."
-          );
-          process.exit(1);
-        }
+      // Get configuration values with precedence: command-line > config defaults > built-in defaults
+      const strategy =
+        parsedOptions.strategy ?? config.defaults?.upload?.strategy ?? "fast";
+      const parallel =
+        parsedOptions.parallel ?? config.defaults?.upload?.parallel ?? 100;
 
-        // Get configuration values with precedence: command-line > config defaults > built-in defaults
-        const strategy =
-          parsedOptions.strategy ?? config.defaults?.upload?.strategy ?? "fast";
-        const parallel =
-          parsedOptions.parallel ?? config.defaults?.upload?.parallel ?? 100;
-
-        const metadata = validateMetadata(parsedOptions.metadata);
-
-        // Collect all files matching patterns
-        const files: string[] = [];
-        for (const pattern of parsedOptions.patterns) {
-          const matches = await glob(pattern, {
-            nodir: true,
-            absolute: false,
-          });
-          files.push(...matches);
-        }
-        // Remove duplicates
-        const uniqueFiles = [...new Set(files)];
+      const metadata = validateMetadata(parsedOptions.metadata);
 
-        if (parsedOptions.patterns) {
-          if (uniqueFiles.length === 0) {
-            log.warn("No files found matching the patterns.");
-            return;
-          }
+      // Collect all files matching patterns
+      const files: string[] = [];
+      for (const pattern of parsedOptions.patterns) {
+        const matches = await glob(pattern, {
+          nodir: true,
+          absolute: false,
+        });
+        files.push(...matches);
+      }
+      // Remove duplicates
+      const uniqueFiles = [...new Set(files)];
 
-          const totalSize = uniqueFiles.reduce((sum, file) => {
-            try {
-              return sum + statSync(file).size;
-            } catch {
-              return sum;
-            }
-          }, 0);
+      if (uniqueFiles.length === 0) {
+        log.warn("No files found matching the patterns.");
+        return;
+      }
 
-          console.log(
-            `Found ${formatCountWithSuffix(uniqueFiles.length, "file")} matching the ${
-              patterns.length > 1 ? "patterns" : "pattern"
-            } (${formatBytes(totalSize)})`
-          );
+      let totalSize = 0;
+      for (const file of uniqueFiles) {
+        try {
+          totalSize += (await stat(file)).size;
+        } catch {
+          // File may not exist
         }
+      }
 
-        if (parsedOptions.dryRun) {
-          console.log(chalk.blue("Dry run - files that would be uploaded:"));
-          uniqueFiles.forEach((file) => {
-            try {
-              const stats = statSync(file);
-              console.log(`  \n${file} (${formatBytes(stats.size)})`);
-              console.log(`    Strategy: ${strategy}`);
-
-              if (metadata && Object.keys(metadata).length > 0) {
-                console.log(`    Metadata: ${JSON.stringify(metadata)}`);
-              }
-            } catch (_error) {
-              console.log(`  ${file} (${chalk.red("✗ File not found")})`);
-            }
-          });
-          return;
-        }
+      console.log(
+        `Found ${formatCountWithSuffix(uniqueFiles.length, "file")} matching the ${
+          patterns.length > 1 ? "patterns" : "pattern"
+        } (${formatBytes(totalSize)})`
+      );
 
-        // Handle --unique flag: check for existing files
-        let existingFiles: Map<string, string> = new Map();
-        if (parsedOptions.unique) {
-          const uniqueSpinner = spinner();
-          uniqueSpinner.start("Checking for existing files...");
+      if (parsedOptions.dryRun) {
+        console.log(chalk.blue("Dry run - files that would be uploaded:"));
+        for (const file of uniqueFiles) {
           try {
-            const storeFiles = await getStoreFiles(client, store.id);
-            existingFiles = new Map(
-              storeFiles
-                .filter((f) => {
-                  const filePath =
-                    typeof f.metadata === "object" &&
-                    f.metadata &&
-                    "file_path" in f.metadata &&
-                    (f.metadata.file_path as string);
-
-                  return filePath && files.includes(filePath);
-                })
-                .map((f) => [
-                  (f.metadata as { file_path: string }).file_path,
-                  f.id,
-                ])
-            );
-            uniqueSpinner.stop(
-              `Found ${formatCountWithSuffix(existingFiles.size, "existing file")}`
-            );
-          } catch (error) {
-            uniqueSpinner.stop();
-            log.error("Failed to check existing files");
-            throw error;
+            const stats = await stat(file);
+            console.log(`  \n${file} (${formatBytes(stats.size)})`);
+            console.log(`    Strategy: ${strategy}`);
+
+            if (metadata && Object.keys(metadata).length > 0) {
+              console.log(`    Metadata: ${JSON.stringify(metadata)}`);
+            }
+          } catch (_error) {
+            console.log(`  ${file} (${chalk.red("✗ File not found")})`);
           }
         }
+        return;
+      }
 
-        // Transform files to shared format
-        const filesToUpload: FileToUpload[] = uniqueFiles.map((filePath) => ({
-          path: filePath,
-          strategy,
-          metadata,
-        }));
-
-        // Upload files with progress tracking
-        await uploadFilesInBatch(client, store.id, filesToUpload, {
-          unique: parsedOptions.unique || false,
-          existingFiles,
-          parallel,
-        });
-      } catch (error) {
-        if (error instanceof Error) {
-          log.error(error.message);
-        } else {
-          log.error("Failed to upload files");
+      // Handle --unique flag: check for existing files
+      let existingFiles: Map<string, string> = new Map();
+      if (parsedOptions.unique) {
+        activeSpinner = spinner();
+        activeSpinner.start("Checking for existing files...");
+        try {
+          existingFiles = await checkExistingFiles(
+            client,
+            store.id,
+            uniqueFiles
+          );
+          activeSpinner.stop(
+            `Found ${formatCountWithSuffix(existingFiles.size, "existing file")}`
+          );
+          activeSpinner = null;
+        } catch (error) {
+          activeSpinner.stop();
+          activeSpinner = null;
+          log.error("Failed to check existing files");
+          throw error;
         }
-        process.exit(1);
       }
+
+      // Transform files to shared format
+      const filesToUpload: FileToUpload[] = uniqueFiles.map((filePath) => ({
+        path: filePath,
+        strategy,
+        metadata,
+      }));
+
+      // Upload files with progress tracking
+      await uploadFilesInBatch(client, store.id, filesToUpload, {
+        unique: parsedOptions.unique || false,
+        existingFiles,
+        parallel,
+      });
+    } catch (error) {
+      activeSpinner?.stop();
+      if (error instanceof Error) {
+        log.error(error.message);
+      } else {
+        log.error("Failed to upload files");
+      }
+      process.exit(1);
     }
-  );
+  });
 
   return command;
 }
diff --git a/packages/cli/src/utils/config.ts b/packages/cli/src/utils/config.ts
index 36706b8..e0c2203 100644
--- a/packages/cli/src/utils/config.ts
+++ b/packages/cli/src/utils/config.ts
@@ -1,4 +1,12 @@
-import { existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
+import { randomBytes } from "node:crypto";
+import {
+  existsSync,
+  mkdirSync,
+  readFileSync,
+  renameSync,
+  unlinkSync,
+  writeFileSync,
+} from "node:fs";
 import { homedir, platform } from "node:os";
 import { join } from "node:path";
 import chalk from "chalk";
@@ -99,7 +107,7 @@ const DEFAULT_CONFIG: CLIConfig = {
       top_k: 10,
       rerank: false,
     },
-    api_key: null,
+    api_key: undefined,
   },
   aliases: {},
 };
@@ -142,7 +150,19 @@ export function saveConfig(config: CLIConfig): void {
     mkdirSync(CONFIG_DIR, { recursive: true });
   }
 
-  writeFileSync(CONFIG_FILE, JSON.stringify(config, null, 2));
+  // Atomic write: write to temp file, then rename
+  const tempFile = `${CONFIG_FILE}.${randomBytes(6).toString("hex")}.tmp`;
+  try {
+    writeFileSync(tempFile, JSON.stringify(config, null, 2));
+    renameSync(tempFile, CONFIG_FILE);
+  } catch (error) {
+    try {
+      unlinkSync(tempFile);
+    } catch {
+      // Ignore cleanup errors
+    }
+    throw error;
+  }
 }
 
 function formatAvailableKeys(config: CLIConfig): string {
diff --git a/packages/cli/src/utils/global-options.ts b/packages/cli/src/utils/global-options.ts
index 46a671b..25ec3fc 100644
--- a/packages/cli/src/utils/global-options.ts
+++ b/packages/cli/src/utils/global-options.ts
@@ -65,33 +65,6 @@ export function addGlobalOptions(command: Command): Command {
     .option("--format <format>", "Output format (table|json|csv)");
 }
 
-export function mergeCommandOptions<T>(command: Command, options: T): T {
-  // Traverse up the command hierarchy to collect all options
-  const allOptions: T[] = [];
-  let currentCommand: Command | null = command;
-
-  // Collect options from all parent commands up to the root
-  while (currentCommand) {
-    if (currentCommand.parent) {
-      allOptions.unshift(currentCommand.parent.opts());
-    }
-    currentCommand = currentCommand.parent;
-  }
-
-  // Add the current command's options last (highest priority)
-  allOptions.push(options);
-
-  // Merge all options, with later options taking priority
-  const merged = Object.assign({}, ...allOptions);
-
-  if (process.env.MXBAI_DEBUG === "true") {
-    console.log("\nCommand hierarchy options:", allOptions);
-    console.log("Merged options:", merged);
-  }
-
-  return merged;
-}
-
 export function parseOptions<T>(
   schema: z.ZodSchema<T>,
   options: Record<string, unknown>
diff --git a/packages/cli/src/utils/logger.ts b/packages/cli/src/utils/logger.ts
new file mode 100644
index 0000000..a776c87
--- /dev/null
+++ b/packages/cli/src/utils/logger.ts
@@ -0,0 +1,21 @@
+import {
+  log as clackLog,
+  spinner as clackSpinner,
+  type SpinnerOptions,
+} from "@clack/prompts";
+
+const stderrOpts = { output: process.stderr } as const;
+
+export const log = {
+  message: (message?: string, opts = {}) =>
+    clackLog.message(message, { ...stderrOpts, ...opts }),
+  info: (message: string) => clackLog.info(message, stderrOpts),
+  success: (message: string) => clackLog.success(message, stderrOpts),
+  warn: (message: string) => clackLog.warn(message, stderrOpts),
+  error: (message: string) => clackLog.error(message, stderrOpts),
+  step: (message: string) => clackLog.step(message, stderrOpts),
+};
+
+export function spinner(opts: Omit<SpinnerOptions, "output"> = {}) {
+  return clackSpinner({ ...opts, ...stderrOpts });
+}
diff --git a/packages/cli/src/utils/manifest.ts b/packages/cli/src/utils/manifest.ts
index 7c1b474..c29c931 100644
--- a/packages/cli/src/utils/manifest.ts
+++ b/packages/cli/src/utils/manifest.ts
@@ -1,5 +1,5 @@
-import { readFileSync, statSync } from "node:fs";
-import { log, spinner } from "@clack/prompts";
+import { readFileSync } from "node:fs";
+import { stat } from "node:fs/promises";
 import type { Mixedbread } from "@mixedbread/sdk";
 import chalk from "chalk";
 import { glob } from "glob";
@@ -8,9 +8,10 @@ import { z } from "zod";
 import type { UploadOptions } from "../commands/store/upload";
 import { loadConfig } from "./config";
 import { warnContextualizationDeprecated } from "./deprecation";
+import { log, spinner } from "./logger";
 import { validateMetadata } from "./metadata";
 import { formatBytes, formatCountWithSuffix } from "./output";
-import { getStoreFiles } from "./store";
+import { checkExistingFiles } from "./store";
 import { type FileToUpload, uploadFilesInBatch } from "./upload";
 
 // Manifest file schema
@@ -139,13 +140,14 @@ export async function uploadFromManifest(
     }
     const uniqueFiles = Array.from(uniqueFilesMap.values());
 
-    const totalSize = uniqueFiles.reduce((sum, file) => {
+    let totalSize = 0;
+    for (const file of uniqueFiles) {
       try {
-        return sum + statSync(file.path).size;
+        totalSize += (await stat(file.path)).size;
       } catch {
-        return sum;
+        // File may not exist
       }
-    }, 0);
+    }
 
     console.log(
       `Found ${formatCountWithSuffix(uniqueFiles.length, "file")} matching the patterns (${formatBytes(totalSize)})`
@@ -153,9 +155,9 @@ export async function uploadFromManifest(
 
     if (options.dryRun) {
       console.log(chalk.blue("\nDry run - files that would be uploaded:"));
-      uniqueFiles.forEach((file) => {
+      for (const file of uniqueFiles) {
         try {
-          const stats = statSync(file.path);
+          const stats = await stat(file.path);
           console.log(`  \n${file.path} (${formatBytes(stats.size)})`);
           console.log(`    Strategy: ${file.strategy}`);
 
@@ -165,7 +167,7 @@ export async function uploadFromManifest(
         } catch (_error) {
           console.log(`  ${file.path} (${chalk.red("✗ File not found")})`);
         }
-      });
+      }
       return;
     }
 
@@ -175,21 +177,11 @@ export async function uploadFromManifest(
       const checkSpinner = spinner();
       checkSpinner.start("Checking for existing files...");
       try {
-        const storeFiles = await getStoreFiles(client, storeIdentifier);
-        existingFiles = new Map(
-          storeFiles
-            .filter((f) =>
-              uniqueFiles.some((file) => {
-                const filePath =
-                  typeof f.metadata === "object" &&
-                  f.metadata &&
-                  "file_path" in f.metadata &&
-                  f.metadata.file_path;
-
-                return filePath && filePath === file.path;
-              })
-            )
-            .map((f) => [(f.metadata as { file_path: string }).file_path, f.id])
+        const localPaths = uniqueFiles.map((file) => file.path);
+        existingFiles = await checkExistingFiles(
+          client,
+          storeIdentifier,
+          localPaths
         );
         checkSpinner.stop(
           `Found ${formatCountWithSuffix(existingFiles.size, "existing file")}`
@@ -206,6 +198,7 @@ export async function uploadFromManifest(
       unique: options.unique || false,
       existingFiles,
       parallel: options.parallel ?? config.defaults.upload.parallel ?? 100,
+      showStrategyPerFile: true,
     });
   } catch (error) {
     if (error instanceof z.ZodError) {
diff --git a/packages/cli/src/utils/output.ts b/packages/cli/src/utils/output.ts
index 0a05971..22623fb 100644
--- a/packages/cli/src/utils/output.ts
+++ b/packages/cli/src/utils/output.ts
@@ -96,13 +96,8 @@ function escapeCsv(value: string): string {
 }
 
 export function formatBytes(bytes: number | undefined): string {
-  if (
-    bytes === 0 ||
-    bytes === undefined ||
-    bytes === null ||
-    Number.isNaN(bytes)
-  )
-    return "0 B";
+  if (bytes === undefined || bytes === null || Number.isNaN(bytes)) return "-";
+  if (bytes === 0) return "0 B";
   const k = 1024;
   const sizes = ["B", "KB", "MB", "GB", "TB"];
   const i = Math.floor(Math.log(Math.abs(bytes)) / Math.log(k));
diff --git a/packages/cli/src/utils/store.ts b/packages/cli/src/utils/store.ts
index c39e982..dea1d8a 100644
--- a/packages/cli/src/utils/store.ts
+++ b/packages/cli/src/utils/store.ts
@@ -94,6 +94,27 @@ export function buildStoreConfig(
   return { contextualization: true };
 }
 
+export async function checkExistingFiles(
+  client: Mixedbread,
+  storeIdentifier: string,
+  localPaths: string[]
+): Promise<Map<string, string>> {
+  const pathSet = new Set(localPaths);
+  const storeFiles = await getStoreFiles(client, storeIdentifier);
+  return new Map(
+    storeFiles
+      .filter((f) => {
+        const filePath =
+          typeof f.metadata === "object" &&
+          f.metadata &&
+          "file_path" in f.metadata &&
+          (f.metadata.file_path as string);
+        return filePath && pathSet.has(filePath);
+      })
+      .map((f) => [(f.metadata as { file_path: string }).file_path, f.id])
+  );
+}
+
 export async function getStoreFiles(
   client: Mixedbread,
   storeIdentifier: string
diff --git a/packages/cli/src/utils/sync.ts b/packages/cli/src/utils/sync.ts
index 1aedefb..a25e2c8 100644
--- a/packages/cli/src/utils/sync.ts
+++ b/packages/cli/src/utils/sync.ts
@@ -1,7 +1,5 @@
-import { statSync } from "node:fs";
 import fs from "node:fs/promises";
 import path from "node:path";
-import { log } from "@clack/prompts";
 import type Mixedbread from "@mixedbread/sdk";
 import type { FileCreateParams } from "@mixedbread/sdk/resources/stores";
 import chalk from "chalk";
@@ -9,6 +7,7 @@ import { glob } from "glob";
 import pLimit from "p-limit";
 import { getChangedFiles, normalizeGitPatterns } from "./git";
 import { calculateFileHash, hashesMatch } from "./hash";
+import { log } from "./logger";
 import { formatBytes, formatCountWithSuffix } from "./output";
 import { buildFileSyncMetadata, type SyncedFileByPath } from "./sync-state";
 import { uploadFile } from "./upload";
@@ -355,7 +354,7 @@ export async function executeSyncChanges(
           };
 
           // Check if file is empty
-          const stats = statSync(file.path);
+          const stats = await fs.stat(file.path);
           if (stats.size === 0) {
             completed++;
             log.warn(
diff --git a/packages/cli/src/utils/update-checker.ts b/packages/cli/src/utils/update-checker.ts
index d69d409..50152d5 100644
--- a/packages/cli/src/utils/update-checker.ts
+++ b/packages/cli/src/utils/update-checker.ts
@@ -1,14 +1,14 @@
 import { existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
-import { homedir } from "node:os";
 import { join } from "node:path";
 import chalk from "chalk";
+import { getConfigDir } from "./config";
 
 interface UpdateCheckCache {
   lastCheck: number;
   latestVersion: string;
 }
 
-const CACHE_DIR = join(homedir(), ".config", "mxbai");
+const CACHE_DIR = getConfigDir();
 const CACHE_FILE = join(CACHE_DIR, "update-check.json");
 const CHECK_INTERVAL = 24 * 60 * 60 * 1000; // 24 hours
 const REGISTRY_URL = "https://registry.npmjs.org/@mixedbread/cli/latest";
@@ -104,13 +104,15 @@ function stripAnsi(str: string): string {
 }
 
 /**
- * Check for updates and display notification if available
- * This runs asynchronously and doesn't block command execution
+ * Check for updates and return a notification banner if available.
+ * Returns the banner string if an update is available, or null otherwise.
  */
-export async function checkForUpdates(currentVersion: string): Promise<void> {
+export async function checkForUpdates(
+  currentVersion: string
+): Promise<string | null> {
   // Skip in CI or non-TTY environments
   if (process.env.CI || !process.stdout.isTTY) {
-    return;
+    return null;
   }
 
   try {
@@ -127,10 +129,11 @@ export async function checkForUpdates(currentVersion: string): Promise<void> {
     }
 
     if (isVersionLessThan(currentVersion, latestVersion)) {
-      console.log(formatUpdateBanner(currentVersion, latestVersion));
-      console.log(); // Add spacing after banner
+      return formatUpdateBanner(currentVersion, latestVersion);
     }
   } catch {
     // Silently fail - update checks should never break the CLI
   }
+
+  return null;
 }
diff --git a/packages/cli/src/utils/upload.ts b/packages/cli/src/utils/upload.ts
index b3c8d5e..4c0270a 100644
--- a/packages/cli/src/utils/upload.ts
+++ b/packages/cli/src/utils/upload.ts
@@ -1,10 +1,11 @@
-import { readFileSync, statSync } from "node:fs";
+import { readFile, stat } from "node:fs/promises";
 import { basename, relative } from "node:path";
-import { log } from "@clack/prompts";
 import type Mixedbread from "@mixedbread/sdk";
 import type { FileCreateParams } from "@mixedbread/sdk/resources/stores";
 import chalk from "chalk";
 import { lookup } from "mime-types";
+import pLimit from "p-limit";
+import { log } from "./logger";
 import { formatBytes, formatCountWithSuffix } from "./output";
 
 export const UPLOAD_TIMEOUT = 1000 * 60 * 10; // 10 minutes
@@ -72,7 +73,7 @@ export async function uploadFile(
   const { metadata = {}, strategy, externalId } = options;
 
   // Read file content
-  const fileContent = readFileSync(filePath);
+  const fileContent = await readFile(filePath);
   const fileName = basename(filePath);
   const mimeType = lookup(filePath) || "application/octet-stream";
   const file = fixMimeTypes(
@@ -104,14 +105,15 @@ export async function uploadFilesInBatch(
     unique: boolean;
     existingFiles: Map<string, string>;
     parallel: number;
+    showStrategyPerFile?: boolean;
   }
 ): Promise<UploadResults> {
-  const { unique, existingFiles, parallel } = options;
-
-  // Detect if this is a manifest upload
-  const isManifestUpload = files.some(
-    (file) => file.metadata?.manifest_entry === true
-  );
+  const {
+    unique,
+    existingFiles,
+    parallel,
+    showStrategyPerFile = false,
+  } = options;
 
   console.log(
     `\nUploading ${formatCountWithSuffix(files.length, "file")} to store...`
@@ -125,89 +127,83 @@ export async function uploadFilesInBatch(
     successfulSize: 0,
   };
 
-  const totalBatches = Math.ceil(files.length / parallel);
-
-  console.log(
-    chalk.gray(
-      `Processing ${totalBatches} batch${totalBatches > 1 ? "es" : ""} (${formatCountWithSuffix(parallel, "file")} per batch)...`
-    )
-  );
-
-  // Process files in batches
-  for (let i = 0; i < files.length; i += parallel) {
-    const batch = files.slice(i, i + parallel);
-    const promises = batch.map(async (file) => {
-      const relativePath = relative(process.cwd(), file.path);
-
-      try {
-        // Delete existing file if using --unique
-        if (unique && existingFiles.has(relativePath)) {
-          const existingFileId = existingFiles.get(relativePath);
-          await client.stores.files.delete(existingFileId, {
-            store_identifier: storeIdentifier,
-          });
-        }
-
-        const fileMetadata = {
-          file_path: relativePath,
-          uploaded_at: new Date().toISOString(),
-          ...file.metadata,
-        };
-
-        // Check if file is empty
-        const stats = statSync(file.path);
-        if (stats.size === 0) {
-          log.warn(`${relativePath} - Empty file skipped`);
-          results.skipped++;
-          return;
-        }
-
-        const fileContent = readFileSync(file.path);
-        const fileName = basename(file.path);
-        const mimeType = lookup(file.path) || "application/octet-stream";
-        const fileToUpload = fixMimeTypes(
-          new File([fileContent], fileName, {
-            type: mimeType,
-          })
-        );
-
-        await client.stores.files.upload(
-          storeIdentifier,
-          fileToUpload,
-          {
-            metadata: fileMetadata,
-            config: {
-              parsing_strategy: file.strategy,
+  console.log(chalk.gray(`Processing with concurrency ${parallel}...`));
+
+  // Process files with sliding-window concurrency
+  const limit = pLimit(parallel);
+  await Promise.allSettled(
+    files.map((file) =>
+      limit(async () => {
+        const relativePath = relative(process.cwd(), file.path);
+
+        try {
+          // Delete existing file if using --unique
+          if (unique && existingFiles.has(relativePath)) {
+            const existingFileId = existingFiles.get(relativePath);
+            await client.stores.files.delete(existingFileId, {
+              store_identifier: storeIdentifier,
+            });
+          }
+
+          const fileMetadata = {
+            file_path: relativePath,
+            uploaded_at: new Date().toISOString(),
+            ...file.metadata,
+          };
+
+          // Check if file is empty
+          const stats = await stat(file.path);
+          if (stats.size === 0) {
+            log.warn(`${relativePath} - Empty file skipped`);
+            results.skipped++;
+            return;
+          }
+
+          const fileContent = await readFile(file.path);
+          const fileName = basename(file.path);
+          const mimeType = lookup(file.path) || "application/octet-stream";
+          const fileToUpload = fixMimeTypes(
+            new File([fileContent], fileName, {
+              type: mimeType,
+            })
+          );
+
+          await client.stores.files.upload(
+            storeIdentifier,
+            fileToUpload,
+            {
+              metadata: fileMetadata,
+              config: {
+                parsing_strategy: file.strategy,
+              },
             },
-          },
-          { timeout: UPLOAD_TIMEOUT }
-        );
-
-        if (unique && existingFiles.has(relativePath)) {
-          results.updated++;
-        } else {
-          results.uploaded++;
-        }
+            { timeout: UPLOAD_TIMEOUT }
+          );
 
-        results.successfulSize += stats.size;
+          if (unique && existingFiles.has(relativePath)) {
+            results.updated++;
+          } else {
+            results.uploaded++;
+          }
 
-        let successMessage = `${relativePath} (${formatBytes(stats.size)})`;
+          results.successfulSize += stats.size;
 
-        if (isManifestUpload) {
-          successMessage += ` [${file.strategy}]`;
-        }
+          let successMessage = `${relativePath} (${formatBytes(stats.size)})`;
 
-        log.success(successMessage);
-      } catch (error) {
-        results.failed++;
-        const errorMsg =
-          error instanceof Error ? error.message : "Unknown error";
-        log.error(`${relativePath} - ${errorMsg}`);
-      }
-    });
+          if (showStrategyPerFile) {
+            successMessage += ` [${file.strategy}]`;
+          }
 
-    await Promise.all(promises);
-  }
+          log.success(successMessage);
+        } catch (error) {
+          results.failed++;
+          const errorMsg =
+            error instanceof Error ? error.message : "Unknown error";
+          log.error(`${relativePath} - ${errorMsg}`);
+        }
+      })
+    )
+  );
 
   // Summary
   console.log(`\n${chalk.bold("Upload Summary:")}`);
@@ -235,7 +231,7 @@ export async function uploadFilesInBatch(
     );
   }
 
-  if (!isManifestUpload && files.length > 0) {
+  if (!showStrategyPerFile && files.length > 0) {
     const firstFile = files[0];
     console.log(chalk.gray(`Strategy: ${firstFile.strategy}`));
   }
diff --git a/packages/cli/tests/commands/store/list.test.ts b/packages/cli/tests/commands/store/list.test.ts
index e86b2f2..0666c84 100644
--- a/packages/cli/tests/commands/store/list.test.ts
+++ b/packages/cli/tests/commands/store/list.test.ts
@@ -493,7 +493,7 @@ describe("Store List Command", () => {
         name: "store1",
         status: "active",
         files: undefined,
-        usage: "0 B",
+        usage: "-",
         created: "1/1/2024",
       });
     });
diff --git a/packages/cli/tests/commands/store/upload.test.ts b/packages/cli/tests/commands/store/upload.test.ts
index 9e38b16..52464c1 100644
--- a/packages/cli/tests/commands/store/upload.test.ts
+++ b/packages/cli/tests/commands/store/upload.test.ts
@@ -37,9 +37,10 @@ const mockCreateClient = clientUtils.createClient as jest.MockedFunction<
 const mockResolveStore = storeUtils.resolveStore as jest.MockedFunction<
   typeof storeUtils.resolveStore
 >;
-const mockGetStoreFiles = storeUtils.getStoreFiles as jest.MockedFunction<
-  typeof storeUtils.getStoreFiles
->;
+const mockCheckExistingFiles =
+  storeUtils.checkExistingFiles as jest.MockedFunction<
+    typeof storeUtils.checkExistingFiles
+  >;
 const mockLoadConfig = configUtils.loadConfig as jest.MockedFunction<
   typeof configUtils.loadConfig
 >;
@@ -352,14 +353,9 @@ describe("Store Upload Command", () => {
         "test.md",
       ]);
 
-      mockGetStoreFiles.mockResolvedValue([
-        {
-          id: "existing_file_id",
-          store_id: "550e8400-e29b-41d4-a716-446655440130",
-          created_at: "2021-02-18T12:00:00Z",
-          metadata: { file_path: "test.md" },
-        },
-      ]);
+      mockCheckExistingFiles.mockResolvedValue(
+        new Map([["test.md", "existing_file_id"]])
+      );
 
       mockClient.stores.files.delete.mockResolvedValue({});
 
@@ -371,9 +367,10 @@ describe("Store Upload Command", () => {
         "--unique",
       ]);
 
-      expect(mockGetStoreFiles).toHaveBeenCalledWith(
+      expect(mockCheckExistingFiles).toHaveBeenCalledWith(
         expect.any(Object),
-        "550e8400-e29b-41d4-a716-446655440130"
+        "550e8400-e29b-41d4-a716-446655440130",
+        ["test.md"]
       );
       expect(mockUploadFilesInBatch).toHaveBeenCalledWith(
         expect.any(Object),
@@ -394,7 +391,7 @@ describe("Store Upload Command", () => {
       (glob as unknown as jest.MockedFunction<typeof glob>).mockResolvedValue([
         "test.md",
       ]);
-      mockGetStoreFiles.mockRejectedValue(new Error("List failed"));
+      mockCheckExistingFiles.mockRejectedValue(new Error("List failed"));
 
       await command.parseAsync([
         "node",
@@ -604,14 +601,9 @@ describe("Store Upload Command", () => {
         "empty.md",
       ]);
 
-      mockGetStoreFiles.mockResolvedValue([
-        {
-          id: "existing_file_id",
-          store_id: "550e8400-e29b-41d4-a716-446655440130",
-          created_at: "2021-02-18T12:00:00Z",
-          metadata: { file_path: "existing.md" },
-        },
-      ]);
+      mockCheckExistingFiles.mockResolvedValue(
+        new Map([["existing.md", "existing_file_id"]])
+      );
 
       // Mock uploadFilesInBatch to return updated and skipped
       mockUploadFilesInBatch.mockResolvedValue({
diff --git a/packages/cli/tests/utils/global-options.test.ts b/packages/cli/tests/utils/global-options.test.ts
index b8dac9b..a5766de 100644
--- a/packages/cli/tests/utils/global-options.test.ts
+++ b/packages/cli/tests/utils/global-options.test.ts
@@ -1,10 +1,9 @@
-import { beforeEach, describe, expect, it, jest } from "@jest/globals";
+import { describe, expect, it } from "@jest/globals";
 import { Command } from "commander";
 import { z } from "zod";
 import {
   BaseGlobalOptionsSchema,
   GlobalOptionsSchema,
-  mergeCommandOptions,
   parseOptions,
   setupGlobalOptions,
 } from "../../src/utils/global-options";
@@ -72,74 +71,6 @@ describe("Global Options", () => {
     });
   });
 
-  describe("mergeCommandOptions", () => {
-    let parentCommand: Command;
-    let childCommand: Command;
-
-    beforeEach(() => {
-      parentCommand = new Command();
-      parentCommand.opts = jest
-        .fn<() => Record<string, unknown>>()
-        .mockReturnValue({ apiKey: "parent_key", format: "json" }) as any;
-
-      childCommand = new Command();
-      childCommand.parent = parentCommand;
-    });
-
-    it("should merge parent and child options", () => {
-      const options = { debug: true };
-      const merged = mergeCommandOptions(childCommand, options);
-
-      expect(merged).toEqual({
-        apiKey: "parent_key",
-        format: "json",
-        debug: true,
-      });
-    });
-
-    it("should prioritize child options over parent", () => {
-      const options = { apiKey: "child_key", format: "csv" };
-      const merged = mergeCommandOptions(childCommand, options);
-
-      expect(merged).toEqual({
-        apiKey: "child_key",
-        format: "csv",
-      });
-    });
-
-    it("should handle commands without parent", () => {
-      const command = new Command();
-      const options = { apiKey: "test_key" };
-      const merged = mergeCommandOptions(command, options);
-
-      expect(merged).toEqual({ apiKey: "test_key" });
-    });
-
-    it("should log options in debug mode", () => {
-      const originalDebug = process.env.MXBAI_DEBUG;
-      process.env.MXBAI_DEBUG = "true";
-
-      const options = { debug: true };
-      mergeCommandOptions(childCommand, options);
-
-      expect(console.log).toHaveBeenCalledWith(
-        "\nCommand hierarchy options:",
-        expect.any(Array)
-      );
-      expect(console.log).toHaveBeenCalledWith(
-        "Merged options:",
-        expect.any(Object)
-      );
-
-      // Cleanup
-      if (originalDebug) {
-        process.env.MXBAI_DEBUG = originalDebug;
-      } else {
-        delete process.env.MXBAI_DEBUG;
-      }
-    });
-  });
-
   describe("parseOptions", () => {
     it("should parse valid options", () => {
       const options = {
diff --git a/packages/cli/tests/utils/output.test.ts b/packages/cli/tests/utils/output.test.ts
index 6e979d8..edb8ecd 100644
--- a/packages/cli/tests/utils/output.test.ts
+++ b/packages/cli/tests/utils/output.test.ts
@@ -30,6 +30,11 @@ describe("Output Utils", () => {
       expect(formatBytes(-1048576)).toBe("-1 MB");
     });
 
+    it("should return dash for undefined, null, and NaN", () => {
+      expect(formatBytes(undefined)).toBe("-");
+      expect(formatBytes(NaN)).toBe("-");
+    });
+
     it("should round to two decimal places", () => {
       expect(formatBytes(1126)).toBe("1.1 KB");
       expect(formatBytes(1229)).toBe("1.2 KB");
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
index 5810640..7d8435d 100644
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -44,9 +44,6 @@ importers:
       commander:
         specifier: ^14.0.3
         version: 14.0.3
-      dotenv:
-        specifier: ^17.3.1
-        version: 17.3.1
       glob:
         specifier: ^13.0.3
         version: 13.0.3
@@ -1718,10 +1715,6 @@ packages:
     resolution: {integrity: sha512-WkrWp9GR4KXfKGYzOLmTuGVi1UWFfws377n9cc55/tb6DuqyF6pcQ5AbiHEshaDpY9v6oaSr2XCDidGmMwdzIA==}
     engines: {node: '>=8'}
 
-  dotenv@17.3.1:
-    resolution: {integrity: sha512-IO8C/dzEb6O3F9/twg6ZLXz164a2fhTnEWb95H23Dm4OuN+92NmEAlTrupP9VW6Jm3sO26tQlqyvyi4CsnY9GA==}
-    engines: {node: '>=12'}
-
   eastasianwidth@0.2.0:
     resolution: {integrity: sha512-I88TYZWc9XiYHRQ4/3c5rjjfgkjhLyW2luGIheGERbNQ6OY7yTybanSpDXZa8y7VUP9YmDcYa+eyq4ca7iLqWA==}
 
@@ -4958,8 +4951,6 @@ snapshots:
     dependencies:
       path-type: 4.0.0
 
-  dotenv@17.3.1: {}
-
   eastasianwidth@0.2.0: {}
 
   electron-to-chromium@1.5.286: {}