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Changes BookmarkAppHelper, CrxInstaller, and ConvertWebAppToExtension
so that clients can set the manifest location and extra install flags
that will be used when creating the extension.

Bug: 852244

Change-Id: I59077e015dc80d9461218f3722942e58e9bc5281
Reviewed-on: https://chromium-review.googlesource.com/1170152Reviewed-by: Devlin <rdevlin.cronin@chromium.org>
Commit-Queue: Giovanni Ortuño Urquidi <ortuno@chromium.org>
Cr-Commit-Position: refs/heads/master@{#582513}