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This CL moves Zucchini-gen invocation code from zucchini_commands.cc
(in target zucchini) to zucchini_integration.cc (in target zucchini_io)
to clean up layering in Zucchini API, i.e.:
- zucchini_lib: Operates on buffers only.
- zucchini_io: Adds files interface, uses memory-mapped I/O.
- zucchini: Stand-alone executable that parses command-line arguments.

Other changes:
- Rename zucchini_lib functions (zuchcini.h), to dedup names and
  emphasize that these functions operate on buffers:
  - GenerateEnsemble() -> GenerateBuffer(),
  - GenerateEnsembleWithImposedMatches() -> GenerateBufferImposed(),
  - GenerateRaw() -> GenerateBufferRaw(),
  - Apply() -> ApplyBuffer().
  These renames only affect Zucchini and various tests.
- Variable renames and parameter reordering in zucchini_integration.cc.
- Remove '-dd' param in help text of Zucchini-detect (was never ported
  from Trunk, and has been recently deleted there as well).
- Replace all base::File&& with base::File.
- Miscellaneous cleanup for header include.
- Update README.md.

Change-Id: I835b80d4d3d7b291fa822a7a89dab225bf9171e9
Reviewed-on: https://chromium-review.googlesource.com/1105625Reviewed-by: Samuel Huang <huangs@chromium.org>
Reviewed-by: Greg Thompson <grt@chromium.org>
Commit-Queue: Samuel Huang <huangs@chromium.org>
Cr-Commit-Position: refs/heads/master@{#569274}