fix: mid-file blank context misidentified as EOF

apply.go

@@ -149,9 +149,24 @@ func matchFragment(source []fileLine, start int, fragment []fileLine, ignoreWhit
 }
 
 func lineMatches(left, right fileLine, ignoreWhitespace bool) bool {
-	if left.hasNewline != right.hasNewline || left.eofMarker != right.eofMarker {
+	if left.hasNewline != right.hasNewline {
 		return false
 	}
+
+	if left.eofMarker != right.eofMarker {
+		// eofMarker is unreliable on blank lines: a mid-file blank and the
+		// synthetic source-EOF sentinel both serialize as " \n" in unified
+		// diff, so the parser can't tell them apart. We accept the position
+		// match here; applyHunk then writes the correct eofMarker by copying
+		// it from the matched source line instead of the patch line.
+		isBlankWithNewLine := func(line fileLine) bool {
+			return line.text == "" && line.hasNewline
+		}
+
+		if !isBlankWithNewLine(left) || !isBlankWithNewLine(right) {
+			return false
+		}
+	}
 	if left.text == right.text {
 		return true
 	}

apply_result.go

@@ -31,7 +31,13 @@ type applyConflict struct {
 
 // applyError reports the aggregate apply outcome.
 type applyError struct {
-	DirectMisses   int
+	// DirectMisses counts hunks whose preimage could not be located in the
+	// pristine file during a direct (non-merge) apply. The output content is
+	// left unchanged for those regions; no conflict markers are emitted.
+	DirectMisses int
+	// MergeConflicts counts hunks whose preimage could not be located during
+	// a merge-mode apply. The output content contains git-style conflict
+	// markers (<<<<<<<, =======, >>>>>>>) around each affected region.
 	MergeConflicts int
 	// ConflictingHunks keeps the legacy count available for callers that still
 	// reason about conflict hunks rather than the new miss/conflict split.

apply_session.go

@@ -87,7 +87,16 @@ func (s *applySession) applyHunk(hunk patchHunk, match matchedHunk) {
 	for _, hunkLine := range hunk.lines[match.hunkStart:match.hunkEnd] {
 		switch hunkLine.kind {
 		case ' ':
-			s.image = append(s.image, fileLine{text: hunkLine.text, hasNewline: hunkLine.hasNewline, eofMarker: hunkLine.newEOF})
+			// Source eofMarker from the matched source line. The parser's
+			// hunkLine.newEOF flag is unreliable for blank trailing context
+			// because markEOFMarkers cannot distinguish a real mid-file
+			// blank context line from the synthetic source EOF marker
+			// (see related comment in lineMatches).
+			eof := hunkLine.newEOF
+			if s.cursor < len(s.sourceLines) {
+				eof = s.sourceLines[s.cursor].eofMarker
+			}
+			s.image = append(s.image, fileLine{text: hunkLine.text, hasNewline: hunkLine.hasNewline, eofMarker: eof})
 			s.cursor++
 		case '-':
 			s.cursor++

apply_test.go

@@ -1019,3 +1019,41 @@ func TestApplyFile_PreservesExactBytes(t *testing.T) {
 	require.NoError(t, err)
 	assert.True(t, bytes.Equal(files.out, applied))
 }
+
+// blankTrailingContextFixture provides a hunk inserting lines between two
+// structural blocks where the trailing context line is blank. markEOFMarkers
+// previously flagged any blank context line at the hunk's count boundary as
+// an EOF marker, causing it to mismatch a real mid-file blank line in source.
+var blankTrailingContextFixture = struct {
+	original []byte
+	target   []byte
+}{
+	original: []byte("class Foo {\n    void a() {}\n\n    void b() {}\n\n    void c() {}\n}\n"),
+	target:   []byte("class Foo {\n    void a() {}\n\n    void b() {}\n\n    void inserted() {}\n\n    void c() {}\n}\n"),
+}
+
+// TestApplyFile_BlankTrailingContextMidFile is a regression test for the
+// fixture above against the direct apply path.
+func TestApplyFile_BlankTrailingContextMidFile(t *testing.T) {
+	t.Parallel()
+
+	f := blankTrailingContextFixture
+	patch := buildPatchWithContext(t, "Foo.java", f.original, f.target, 3)
+	applied, err := ApplyFile(f.original, patch)
+	require.NoError(t, err)
+	assert.Equal(t, f.target, applied)
+}
+
+// TestApplyFile_BlankTrailingContextWithConflicts mirrors the regression test
+// above against the merge mode used by ApplyFileWithConflicts. The bug
+// surfaced as a spurious conflict on a freshly generated file because the
+// hunk's trailing blank context was misidentified as an EOF marker.
+func TestApplyFile_BlankTrailingContextWithConflicts(t *testing.T) {
+	t.Parallel()
+
+	f := blankTrailingContextFixture
+	patch := buildPatchWithContext(t, "Foo.java", f.original, f.target, 3)
+	applied, err := ApplyFileWithConflicts(f.original, patch)
+	require.NoError(t, err)
+	assert.Equal(t, f.target, applied)
+}