thodg/libgit2

diff --git a/src/apply.c b/src/apply.c
index 1a20278..0810c02 100644
--- a/src/apply.c
+++ b/src/apply.c
@@ -386,6 +386,7 @@ done:
 static int apply_one(
 	git_repository *repo,
 	git_reader *preimage_reader,
+	git_index *preimage,
 	git_index *postimage,
 	git_diff *diff,
 	size_t i)
@@ -395,8 +396,8 @@ static int apply_one(
 	const git_diff_delta *delta;
 	char *filename = NULL;
 	unsigned int mode;
-	git_oid blob_id;
-	git_index_entry index_entry;
+	git_oid pre_id, post_id;
+	git_index_entry pre_entry, post_entry;
 	int error;
 
 	if ((error = git_patch_from_diff(&patch, diff, i)) < 0)
@@ -404,11 +405,8 @@ static int apply_one(
 
 	delta = git_patch_get_delta(patch);
 
-	if (delta->status == GIT_DELTA_DELETED)
-		goto done;
-
 	if (delta->status != GIT_DELTA_ADDED) {
-		if ((error = git_reader_read(&pre_contents,
+		if ((error = git_reader_read(&pre_contents, &pre_id,
 		    preimage_reader, delta->old_file.path)) < 0) {
 
 			/* ENOTFOUND is really an application error */
@@ -417,21 +415,44 @@ static int apply_one(
 
 			goto done;
 		}
+
+		/*
+		 * We need to populate the preimage data structure with the
+		 * contents that we are using as the preimage for this file.
+		 * This allows us to apply patches to files that have been
+		 * modified in the working directory.  During checkout,
+		 * we will use this expected preimage as the baseline, and
+		 * limit checkout to only the paths affected by patch
+		 * application.  (Without this, we would fail to write the
+		 * postimage contents to any file that had been modified
+		 * from HEAD on-disk, even if the patch application succeeded.)
+		 */
+		if (preimage) {
+			memset(&pre_entry, 0, sizeof(git_index_entry));
+			pre_entry.path = delta->old_file.path;
+			pre_entry.mode = delta->old_file.mode;
+			git_oid_cpy(&pre_entry.id, &pre_id);
+
+			if ((error = git_index_add(preimage, &pre_entry)) < 0)
+				goto done;
+		}
 	}
 
-	if ((error = git_apply__patch(&post_contents, &filename, &mode,
-			pre_contents.ptr, pre_contents.size, patch)) < 0 ||
-		(error = git_blob_create_frombuffer(&blob_id, repo,
-			post_contents.ptr, post_contents.size)) < 0)
-		goto done;
+	if (delta->status != GIT_DELTA_DELETED) {
+		if ((error = git_apply__patch(&post_contents, &filename, &mode,
+				pre_contents.ptr, pre_contents.size, patch)) < 0 ||
+			(error = git_blob_create_frombuffer(&post_id, repo,
+				post_contents.ptr, post_contents.size)) < 0)
+			goto done;
 
-	memset(&index_entry, 0, sizeof(git_index_entry));
-	index_entry.path = filename;
-	index_entry.mode = mode;
-	git_oid_cpy(&index_entry.id, &blob_id);
+		memset(&post_entry, 0, sizeof(git_index_entry));
+		post_entry.path = filename;
+		post_entry.mode = mode;
+		git_oid_cpy(&post_entry.id, &post_id);
 
-	if ((error = git_index_add(postimage, &index_entry)) < 0)
-		goto done;
+		if ((error = git_index_add(postimage, &post_entry)) < 0)
+			goto done;
+	}
 
 done:
 	git_buf_dispose(&pre_contents);
@@ -483,7 +504,7 @@ int git_apply_to_tree(
 	}
 
 	for (i = 0; i < git_diff_num_deltas(diff); i++) {
-		if ((error = apply_one(repo, pre_reader, postimage, diff, i)) < 0)
+		if ((error = apply_one(repo, pre_reader, NULL, postimage, diff, i)) < 0)
 			goto done;
 	}
 
@@ -501,6 +522,7 @@ done:
 static int git_apply__to_workdir(
 	git_repository *repo,
 	git_diff *diff,
+	git_index *preimage,
 	git_index *postimage,
 	git_apply_options *opts)
 {
@@ -537,6 +559,8 @@ static int git_apply__to_workdir(
 	checkout_opts.paths.strings = (char **)paths.contents;
 	checkout_opts.paths.count = paths.length;
 
+	checkout_opts.baseline_index = preimage;
+
 	error = git_checkout_index(repo, postimage, &checkout_opts);
 
 	/*
@@ -554,6 +578,7 @@ done:
 static int git_apply__to_index(
 	git_repository *repo,
 	git_diff *diff,
+	git_index *preimage,
 	git_index *postimage,
 	git_apply_options *opts)
 {
@@ -563,6 +588,7 @@ static int git_apply__to_index(
 	size_t i;
 	int error;
 
+	GIT_UNUSED(preimage);
 	GIT_UNUSED(opts);
 
 	if ((error = git_repository_index(&index, repo)) < 0)
@@ -615,7 +641,7 @@ int git_apply(
 	git_diff *diff,
 	git_apply_options *given_opts)
 {
-	git_index *postimage = NULL;
+	git_index *preimage = NULL, *postimage = NULL;
 	git_reader *pre_reader = NULL;
 	git_apply_options opts = GIT_APPLY_OPTIONS_INIT;
 	size_t i;
@@ -643,28 +669,30 @@ int git_apply(
 		goto done;
 
 	/*
-	 * Build the postimage differences.  Note that this is not the
-	 * complete postimage, it only contains the new files created
-	 * during the application.  We will limit checkout to only write
-	 * the files affected by this diff.
+	 * Build the preimage and postimage (differences).  Note that
+	 * this is not the complete preimage or postimage, it only
+	 * contains the files affected by the patch.  We want to avoid
+	 * having the full repo index, so we will limit our checkout
+	 * to only write these files that were affected by the diff.
 	 */
-	if ((error = git_index_new(&postimage)) < 0)
+	if ((error = git_index_new(&preimage)) < 0 ||
+	    (error = git_index_new(&postimage)) < 0)
 		goto done;
 
 	for (i = 0; i < git_diff_num_deltas(diff); i++) {
-		if ((error = apply_one(repo, pre_reader, postimage, diff, i)) < 0)
+		if ((error = apply_one(repo, pre_reader, preimage, postimage, diff, i)) < 0)
 			goto done;
 	}
 
 	switch (opts.location) {
 	case GIT_APPLY_LOCATION_BOTH:
-		error = git_apply__to_workdir(repo, diff, postimage, &opts);
+		error = git_apply__to_workdir(repo, diff, preimage, postimage, &opts);
 		break;
 	case GIT_APPLY_LOCATION_INDEX:
-		error = git_apply__to_index(repo, diff, postimage, &opts);
+		error = git_apply__to_index(repo, diff, preimage, postimage, &opts);
 		break;
 	case GIT_APPLY_LOCATION_WORKDIR:
-		error = git_apply__to_workdir(repo, diff, postimage, &opts);
+		error = git_apply__to_workdir(repo, diff, preimage, postimage, &opts);
 		break;
 	default:
 		assert(false);
@@ -675,6 +703,7 @@ int git_apply(
 
 done:
 	git_index_free(postimage);
+	git_index_free(preimage);
 	git_reader_free(pre_reader);
 
 	return error;
diff --git a/src/reader.c b/src/reader.c
index 754b90a..32900df 100644
--- a/src/reader.c
+++ b/src/reader.c
@@ -24,6 +24,7 @@ typedef struct {
 
 static int tree_reader_read(
 	git_buf *out,
+	git_oid *out_id,
 	git_reader *_reader,
 	const char *filename)
 {
@@ -37,6 +38,9 @@ static int tree_reader_read(
 	    (error = git_buf_set(out, git_blob_rawcontent(blob), git_blob_rawsize(blob))) < 0)
 		goto done;
 
+	if (out_id)
+		git_oid_cpy(out_id, git_tree_entry_id(tree_entry));
+
 done:
 	git_blob_free(blob);
 	git_tree_entry_free(tree_entry);
@@ -74,6 +78,7 @@ typedef struct {
 
 static int workdir_reader_read(
 	git_buf *out,
+	git_oid *out_id,
 	git_reader *_reader,
 	const char *filename)
 {
@@ -86,7 +91,11 @@ static int workdir_reader_read(
 		goto done;
 
 	/* TODO: should we read the filtered data? */
-	error = git_futils_readbuffer(out, path.ptr);
+	if ((error = git_futils_readbuffer(out, path.ptr)) < 0)
+		goto done;
+
+	if (out_id)
+		error = git_odb_hash(out_id, out->ptr, out->size, GIT_OBJ_BLOB);
 
 done:
 	git_buf_dispose(&path);
@@ -125,6 +134,7 @@ typedef struct {
 
 static int index_reader_read(
 	git_buf *out,
+	git_oid *out_id,
 	git_reader *_reader,
 	const char *filename)
 {
@@ -139,6 +149,9 @@ static int index_reader_read(
 	if ((error = git_blob_lookup(&blob, reader->repo, &entry->id)) < 0)
 		goto done;
 
+	if (out_id)
+		git_oid_cpy(out_id, &entry->id);
+
 	error = git_blob__getbuf(out, blob);
 
 done:
@@ -185,11 +198,15 @@ int git_reader_for_index(
 
 /* generic */
 
-int git_reader_read(git_buf *out, git_reader *reader, const char *filename)
+int git_reader_read(
+	git_buf *out,
+	git_oid *out_id,
+	git_reader *reader,
+	const char *filename)
 {
 	assert(out && reader && filename);
 
-	return reader->read(out, reader, filename);
+	return reader->read(out, out_id, reader, filename);
 }
 
 void git_reader_free(git_reader *reader)
diff --git a/src/reader.h b/src/reader.h
index 18c7f59..7bb60e1 100644
--- a/src/reader.h
+++ b/src/reader.h
@@ -22,7 +22,7 @@ typedef struct git_reader git_reader;
  * reader after disposing the underlying object that it reads.
  */
 struct git_reader {
-	int (*read)(git_buf *out, git_reader *reader, const char *filename);
+	int (*read)(git_buf *out, git_oid *out_oid, git_reader *reader, const char *filename);
 	void (*free)(git_reader *reader);
 };
 
@@ -89,6 +89,7 @@ extern int git_reader_for_workdir(
  */
 extern int git_reader_read(
 	git_buf *out,
+	git_oid *out_id,
 	git_reader *reader,
 	const char *filename);