Updates merge_target_files soong_zip to use -r instead of -l.

This is needed due to output artifacts in the zip that confuse globbing,
such as [.

(Also changes this call to RunAndCheckOutput, which prints the stderror
by default instead of RunAndWait which does not. Removes RunAndWait
which is now unused)

Bug: 179799226
Test: Run merge_target_files to merge two partial builds
Change-Id: Ibf8a5b0c013c9cd8b1e61195d97583f247d97c6f