gclient flatten: fix an issue with custom_deps
TBR=dpranke Bug: 570091 Change-Id: I1b8cc8156c83c72b2fc599d90059bc7f2674ca17 Reviewed-on: https://chromium-review.googlesource.com/532995Reviewed-by:Paweł Hajdan Jr. <phajdan.jr@chromium.org> Commit-Queue: Paweł Hajdan Jr. <phajdan.jr@chromium.org>
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