[Zucchini] Refactor Zucchini-gen in zucchini_io layer.

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/1105625
Reviewed-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}
NOKEYCHECK=True
GitOrigin-RevId: 9f0f325d6e2595deb8d50c77e0464946f3bf1ec1
diff --git a/zucchini_integration.h b/zucchini_integration.h
index ce98b28..2ae6091 100644
--- a/zucchini_integration.h
+++ b/zucchini_integration.h
@@ -5,28 +5,59 @@
 #ifndef COMPONENTS_ZUCCHINI_ZUCCHINI_INTEGRATION_H_
 #define COMPONENTS_ZUCCHINI_ZUCCHINI_INTEGRATION_H_
 
+#include <string>
+
 #include "base/files/file.h"
 #include "base/files/file_path.h"
 #include "components/zucchini/zucchini.h"
 
+// Zucchini integration interface to wrap core Zucchini library with file I/O.
+
 namespace zucchini {
 
-// Applies the patch in |patch_file| to the bytes in |old_file| and writes the
-// result to |new_file|. Since this uses memory mapped files, crashes are
-// expected in case of I/O errors. On Windows, |new_file| is kept iff returned
+// Generates a patch to transform |old_file| to |new_file|, and writes the
+// result to |patch_file|. Since this uses memory mapped files, crashes are
+// expected in case of I/O errors. On Windows, |patch_file| is kept iff returned
 // code is kStatusSuccess or if |force_keep == true|, and is deleted otherwise.
 // For UNIX systems the caller needs to do cleanup since it has ownership of the
-// base::File params and Zucchini has no knowledge of which base::FilePath to
+// base::File params, and Zucchini has no knowledge of which base::FilePath to
+// delete. If |is_raw == true| then uses Raw Zucchini. If |imposed_matches| is
+// non-empty, then overrides default element detection and matching heuristics
+// with custom element matching encoded in |imposed_matches|, which should be
+// formatted as:
+//   "#+#=#+#,#+#=#+#,..."  (e.g., "1+2=3+4", "1+2=3+4,5+6=7+8"),
+// where "#+#=#+#" encodes a match as 4 unsigned integers:
+//   [offset in "old", size in "old", offset in "new", size in "new"].
+status::Code Generate(base::File old_file,
+                      base::File new_file,
+                      base::File patch_file,
+                      bool force_keep = false,
+                      bool is_raw = false,
+                      std::string imposed_matches = "");
+
+// Alternative Generate() interface that takes base::FilePath as arguments.
+// Performs proper cleanup in Windows and UNIX if failure occurs.
+status::Code Generate(const base::FilePath& old_path,
+                      const base::FilePath& new_path,
+                      const base::FilePath& patch_path,
+                      bool force_keep = false,
+                      bool is_raw = false,
+                      std::string imposed_matches = "");
+
+// Applies the patch in |patch_file| to |old_file|, and writes the result to
+// |new_file|. Since this uses memory mapped files, crashes are expected in case
+// of I/O errors. On Windows, |new_file| is kept iff returned code is
+// kStatusSuccess or if |force_keep == true|, and is deleted otherwise. For UNIX
+// systems the caller needs to do cleanup since it has ownership of the
+// base::File params, and Zucchini has no knowledge of which base::FilePath to
 // delete.
-status::Code Apply(base::File&& old_file,
-                   base::File&& patch_file,
-                   base::File&& new_file,
+status::Code Apply(base::File old_file,
+                   base::File patch_file,
+                   base::File new_file,
                    bool force_keep = false);
 
-// Applies the patch in |patch_path| to the bytes in |old_path| and writes the
-// result to |new_path|. Since this uses memory mapped files, crashes are
-// expected in case of I/O errors. |new_path| is kept iff returned code is
-// kStatusSuccess or if |force_keep == true|, and is deleted otherwise.
+// Alternative Apply() interface that takes base::FilePath as arguments.
+// Performs proper cleanup in Windows and UNIX if failure occurs.
 status::Code Apply(const base::FilePath& old_path,
                    const base::FilePath& patch_path,
                    const base::FilePath& new_path,