diff --git a/src/vs/base/common/arrays.ts b/src/vs/base/common/arrays.ts
index 65187b136fd825506107d3ae10348fb73a0c8b0b..3d92f2bceebaa3218944b391bb8571b44d5b9a3f 100644
--- a/src/vs/base/common/arrays.ts
+++ b/src/vs/base/common/arrays.ts
@@ -257,8 +257,12 @@ export function fill<T>(num: number, valueFn: () => T, arr: T[] = []): T[] {
 	return arr;
 }
 
-export function index<T>(array: T[], indexer: (t: T) => string): { [key: string]: T; } {
-	const result = Object.create(null);
-	array.forEach(t => result[indexer(t)] = t);
-	return result;
+export function index<T>(array: T[], indexer: (t: T) => string): { [key: string]: T; };
+export function index<T,R>(array: T[], indexer: (t: T) => string, merger?: (t: T, r: R) => R): { [key: string]: R; };
+export function index<T,R>(array: T[], indexer: (t: T) => string, merger: (t: T, r: R) => R = t => t as any): { [key: string]: R; } {
+	return array.reduce((r, t) => {
+		const key = indexer(t);
+		r[key] = merger(t, r[key]);
+		return r;
+	}, Object.create(null));
 }
\ No newline at end of file
diff --git a/src/vs/workbench/parts/git/node/git.lib.ts b/src/vs/workbench/parts/git/node/git.lib.ts
index d0922c2b65aebee4afe0f9ad32d2e3ec0462064b..25868a7d08210a638bb92433f7bae68cf5ac36ed 100644
--- a/src/vs/workbench/parts/git/node/git.lib.ts
+++ b/src/vs/workbench/parts/git/node/git.lib.ts
@@ -11,9 +11,10 @@ import * as pfs from 'vs/base/node/pfs';
 import { guessMimeTypes, isBinaryMime } from 'vs/base/common/mime';
 import { IDisposable, toDisposable, dispose } from 'vs/base/common/lifecycle';
 import { assign } from 'vs/base/common/objects';
+import { sequence } from 'vs/base/common/async';
 import { v4 as UUIDv4 } from 'vs/base/common/uuid';
 import { localize } from 'vs/nls';
-import { uniqueFilter } from 'vs/base/common/arrays';
+import { uniqueFilter, index } from 'vs/base/common/arrays';
 import { IRawFileStatus, RefType, IRef, IBranch, IRemote, GitErrorCodes, IPushOptions } from 'vs/workbench/parts/git/common/git';
 import { detectMimesFromStream } from 'vs/base/node/mime';
 import { IFileOperationResult, FileOperationResult } from 'vs/platform/files/common/files';
@@ -447,8 +448,11 @@ export class Repository {
 	}
 
 	clean(paths: string[]): Promise {
-		const args = [ 'clean', '-f', '-q', '--' ].concat(paths);
-		return this.run(args);
+		const byDirname = index<string, string[]>(paths, p => path.dirname(p), (p, r) => (r || []).concat([p]));
+		const groups = Object.keys(byDirname).map(key => byDirname[key]);
+		const tasks = groups.map(group => () => this.run([ 'clean', '-f', '-q', '--' ].concat(group)));
+
+		return sequence(tasks);
 	}
 
 	undo(): Promise {